#------------------------------------------------------------------------------- # 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 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.32403899 grid = 40 40 72 stencil order = 5 estimated absolute RMS force accuracy = 0.0030162601 estimated relative force accuracy = 9.0833777e-06 using double precision KISS FFT 3d grid and FFT values/proc = 11664 4800 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 1.00282 0.127012 8304 2 97.1666 11.588 2768 Per MPI rank memory allocation (min/avg/max) = 11.45 | 12.88 | 13.57 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 4657.6197 132487.99 0.91634748 428.55654 9.5095556 82.520957 0 0 27383.956 69430.099 -314.28581 -271167.58 -174261.5 8088.7858 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.08855e-06 8304 2 103.7 8.74302e-05 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.49371e-06 8304 2 103.7 0.000103475 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.48981e-06 8304 2 103.7 9.26538e-05 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.33768e-06 8304 2 103.7 9.2891e-05 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.27538e-06 8304 2 103.7 9.13856e-05 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.4324e-06 8304 2 103.7 0.000115758 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.55124e-06 8304 2 103.7 0.000108704 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.10516e-06 8304 2 103.7 8.94593e-05 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.43654e-06 8304 2 103.7 9.02974e-05 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.21147e-06 8304 2 103.7 9.77692e-05 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.2639e-06 8304 2 103.7 0.000105529 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.29133e-06 8304 2 103.7 0.000107068 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.22762e-06 8304 2 103.7 9.46529e-05 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.30579e-06 8304 2 103.7 0.000101731 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.50531e-06 8304 2 103.7 0.000115799 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.47377e-06 8304 2 103.7 0.000116082 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.11593e-06 8304 2 103.7 9.45367e-05 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.39248e-06 8304 2 103.7 9.86245e-05 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.22019e-06 8304 2 103.7 9.3541e-05 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.27454e-06 8304 2 103.7 9.10818e-05 2768 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.17652e-06 8304 2 103.7 9.01723e-05 2768 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.74823e-06 8304 2 103.7 0.00011086 2768 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.14056e-06 8304 2 103.7 0.000101698 2768 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.38865e-06 8304 2 103.7 0.000100198 2768 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.17524e-06 8304 2 103.7 0.000104856 2768 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.17368e-06 8304 2 103.7 9.05114e-05 2768 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.44285e-06 8304 2 103.7 0.000103836 2768 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.18474e-06 8304 2 103.7 9.09085e-05 2768 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.37941e-06 8304 2 103.7 9.69329e-05 2768 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.3515e-06 8304 2 103.7 0.000130889 2768 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.16123e-06 8304 2 103.7 9.8626e-05 2768 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.13527e-06 8304 2 103.7 0.000107998 2768 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.08057e-06 8304 2 103.7 9.84602e-05 2768 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.37431e-06 8304 2 103.7 0.000101568 2768 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.14267e-06 8304 2 103.7 9.22812e-05 2768 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.26447e-06 8304 2 103.7 8.99844e-05 2768 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.19135e-06 8304 2 103.7 9.20916e-05 2768 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.09701e-06 8304 2 103.7 9.75782e-05 2768 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.20765e-06 8304 2 103.7 0.000100527 2768 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.18627e-06 8304 2 103.7 0.00010052 2768 SHAKE stats (type/ave/delta/count) on step 2050000 2 0.97 1.32487e-06 8304 2 103.7 9.64438e-05 2768 SHAKE stats (type/ave/delta/count) on step 2100000 2 0.97 1.26075e-06 8304 2 103.7 9.39014e-05 2768 SHAKE stats (type/ave/delta/count) on step 2150000 2 0.97 1.30271e-06 8304 2 103.7 9.03816e-05 2768 SHAKE stats (type/ave/delta/count) on step 2200000 2 0.97 1.27755e-06 8304 2 103.7 9.73173e-05 2768 SHAKE stats (type/ave/delta/count) on step 2250000 2 0.97 1.25071e-06 8304 2 103.7 0.000101212 2768 SHAKE stats (type/ave/delta/count) on step 2300000 2 0.97 1.67807e-06 8304 2 103.7 9.89326e-05 2768 SHAKE stats (type/ave/delta/count) on step 2350000 2 0.97 1.23244e-06 8304 2 103.7 9.94916e-05 2768 SHAKE stats (type/ave/delta/count) on step 2400000 2 0.97 1.2637e-06 8304 2 103.7 9.66076e-05 2768 SHAKE stats (type/ave/delta/count) on step 2450000 2 0.97 1.35634e-06 8304 2 103.7 0.000111394 2768 SHAKE stats (type/ave/delta/count) on step 2500000 2 0.97 1.167e-06 8304 2 103.7 0.000101237 2768 SHAKE stats (type/ave/delta/count) on step 2550000 2 0.97 1.5144e-06 8304 2 103.7 0.000112269 2768 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.97 1.18094e-06 8304 2 103.7 0.000114509 2768 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.97 1.25405e-06 8304 2 103.7 9.17097e-05 2768 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.97 1.01482e-06 8304 2 103.7 0.000100158 2768 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.97 1.79787e-06 8304 2 103.7 0.000102286 2768 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.97 1.23404e-06 8304 2 103.7 8.7115e-05 2768 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.97 1.24771e-06 8304 2 103.7 9.2006e-05 2768 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.97 1.24904e-06 8304 2 103.7 9.51884e-05 2768 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.97 1.09117e-06 8304 2 103.7 9.10318e-05 2768 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.58765e-06 8304 2 103.7 0.000112273 2768 SHAKE stats (type/ave/delta/count) on step 3050000 2 0.97 1.291e-06 8304 2 103.7 9.99371e-05 2768 SHAKE stats (type/ave/delta/count) on step 3100000 2 0.97 1.35094e-06 8304 2 103.7 9.09689e-05 2768 SHAKE stats (type/ave/delta/count) on step 3150000 2 0.97 1.52346e-06 8304 2 103.7 0.000107742 2768 SHAKE stats (type/ave/delta/count) on step 3200000 2 0.97 1.40938e-06 8304 2 103.7 9.88724e-05 2768 SHAKE stats (type/ave/delta/count) on step 3250000 2 0.97 1.31926e-06 8304 2 103.7 9.809e-05 2768 SHAKE stats (type/ave/delta/count) on step 3300000 2 0.97 1.15555e-06 8304 2 103.7 9.69849e-05 2768 SHAKE stats (type/ave/delta/count) on step 3350000 2 0.97 1.28461e-06 8304 2 103.7 0.000101775 2768 SHAKE stats (type/ave/delta/count) on step 3400000 2 0.97 1.12527e-06 8304 2 103.7 8.9909e-05 2768 SHAKE stats (type/ave/delta/count) on step 3450000 2 0.97 1.14815e-06 8304 2 103.7 9.22925e-05 2768 SHAKE stats (type/ave/delta/count) on step 3500000 2 0.97 1.24292e-06 8304 2 103.7 0.000107588 2768 SHAKE stats (type/ave/delta/count) on step 3550000 2 0.97 1.34273e-06 8304 2 103.7 9.11918e-05 2768 SHAKE stats (type/ave/delta/count) on step 3600000 2 0.97 1.17019e-06 8304 2 103.7 9.6948e-05 2768 SHAKE stats (type/ave/delta/count) on step 3650000 2 0.97 1.50553e-06 8304 2 103.7 0.00011285 2768 SHAKE stats (type/ave/delta/count) on step 3700000 2 0.97 1.36647e-06 8304 2 103.7 0.000105928 2768 SHAKE stats (type/ave/delta/count) on step 3750000 2 0.97 1.25609e-06 8304 2 103.7 9.45608e-05 2768 SHAKE stats (type/ave/delta/count) on step 3800000 2 0.97 1.40855e-06 8304 2 103.7 0.000113725 2768 SHAKE stats (type/ave/delta/count) on step 3850000 2 0.97 1.33559e-06 8304 2 103.7 0.000100429 2768 SHAKE stats (type/ave/delta/count) on step 3900000 2 0.97 1.09575e-06 8304 2 103.7 9.7783e-05 2768 SHAKE stats (type/ave/delta/count) on step 3950000 2 0.97 1.26206e-06 8304 2 103.7 9.67062e-05 2768 SHAKE stats (type/ave/delta/count) on step 4000000 2 0.97 1.20492e-06 8304 2 103.7 0.000108684 2768 SHAKE stats (type/ave/delta/count) on step 4050000 2 0.97 1.08178e-06 8304 2 103.7 9.17472e-05 2768 SHAKE stats (type/ave/delta/count) on step 4100000 2 0.97 1.26843e-06 8304 2 103.7 0.000114431 2768 SHAKE stats (type/ave/delta/count) on step 4150000 2 0.97 1.35516e-06 8304 2 103.7 9.83622e-05 2768 SHAKE stats (type/ave/delta/count) on step 4200000 2 0.97 1.14861e-06 8304 2 103.7 9.56064e-05 2768 SHAKE stats (type/ave/delta/count) on step 4250000 2 0.97 1.22288e-06 8304 2 103.7 8.84185e-05 2768 SHAKE stats (type/ave/delta/count) on step 4300000 2 0.97 1.12559e-06 8304 2 103.7 8.97213e-05 2768 SHAKE stats (type/ave/delta/count) on step 4350000 2 0.97 1.31376e-06 8304 2 103.7 0.000113697 2768 SHAKE stats (type/ave/delta/count) on step 4400000 2 0.97 1.24734e-06 8304 2 103.7 9.6096e-05 2768 SHAKE stats (type/ave/delta/count) on step 4450000 2 0.97 1.6981e-06 8304 2 103.7 0.00010249 2768 SHAKE stats (type/ave/delta/count) on step 4500000 2 0.97 1.28236e-06 8304 2 103.7 9.59517e-05 2768 SHAKE stats (type/ave/delta/count) on step 4550000 2 0.97 1.9743e-06 8304 2 103.7 0.000131331 2768 SHAKE stats (type/ave/delta/count) on step 4600000 2 0.97 1.16228e-06 8304 2 103.7 9.44817e-05 2768 SHAKE stats (type/ave/delta/count) on step 4650000 2 0.97 1.28573e-06 8304 2 103.7 9.23003e-05 2768 SHAKE stats (type/ave/delta/count) on step 4700000 2 0.97 1.39522e-06 8304 2 103.7 9.78761e-05 2768 SHAKE stats (type/ave/delta/count) on step 4750000 2 0.97 1.64392e-06 8304 2 103.7 0.000121573 2768 SHAKE stats (type/ave/delta/count) on step 4800000 2 0.97 1.24557e-06 8304 2 103.7 9.5628e-05 2768 SHAKE stats (type/ave/delta/count) on step 4850000 2 0.97 1.37127e-06 8304 2 103.7 9.50221e-05 2768 SHAKE stats (type/ave/delta/count) on step 4900000 2 0.97 1.30819e-06 8304 2 103.7 9.91508e-05 2768 SHAKE stats (type/ave/delta/count) on step 4950000 2 0.97 1.27516e-06 8304 2 103.7 9.63055e-05 2768 SHAKE stats (type/ave/delta/count) on step 5000000 2 0.97 1.2193e-06 8304 2 103.7 9.74464e-05 2768 5000000 5000000 -357.45914 132487.99 0.91634748 297.35236 45.629097 84.835284 0 0 21014.573 89283.434 -314.28581 -271053.21 -160624.74 5612.3739 Loop time of 32900.5 on 32 procs for 5000000 steps with 9101 atoms Performance: 13.131 ns/day, 1.828 hours/ns, 151.974 timesteps/s 98.6% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 98.586 | 10302 | 15281 |5461.2 | 31.31 Bond | 4.9863 | 13.385 | 28.977 | 153.5 | 0.04 Kspace | 12575 | 17588 | 27865 |4212.6 | 53.46 Neigh | 1347.5 | 1350.9 | 1357.7 | 8.9 | 4.11 Comm | 1032.8 | 1465.2 | 1645.4 | 608.3 | 4.45 Output | 0.012147 | 0.01439 | 0.016417 | 1.1 | 0.00 Modify | 1952.4 | 2088.9 | 2431.9 | 410.9 | 6.35 Other | | 92.15 | | | 0.28 Nlocal: 284.406 ave 401 max 0 min Histogram: 4 1 3 0 0 0 1 3 2 18 Nghost: 3955.38 ave 5315 max 2159 min Histogram: 8 0 4 0 0 4 0 4 0 12 Neighs: 76627.7 ave 118819 max 0 min Histogram: 4 1 3 4 0 0 0 0 6 14 Total # of neighbors = 2452087 Ave neighs/atom = 269.4305 Ave special neighs/atom = 1.8929788 Neighbor list builds = 249291 Dangerous builds = 0 undump sci restart 0 dump sci all custom 5000000 2.5.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) = 0.32403899 grid = 40 40 72 stencil order = 5 estimated absolute RMS force accuracy = 0.0030162601 estimated relative force accuracy = 9.0833777e-06 using double precision KISS FFT 3d grid and FFT values/proc = 11664 4800 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 5000000 2 0.97 1.2193e-06 8304 2 103.7 9.74464e-05 2768 Per MPI rank memory allocation (min/avg/max) = 11.63 | 13.19 | 13.57 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 -356.8732 132487.99 0.91634748 297.35236 45.629097 84.835284 0 0 21014.573 89283.434 -314.28581 -271053.21 -160624.74 5612.3739 Loop time of 1.23681e-05 on 32 procs for 0 steps with 9101 atoms 109.7% 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 | | 1.237e-05 | | |100.00 Nlocal: 284.406 ave 401 max 0 min Histogram: 4 1 3 0 0 0 1 3 2 18 Nghost: 3955.38 ave 5315 max 2159 min Histogram: 8 0 4 0 0 4 0 4 0 12 Neighs: 76627.7 ave 118819 max 0 min Histogram: 4 1 3 4 0 0 0 0 6 14 Total # of neighbors = 2452087 Ave neighs/atom = 269.4305 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