#------------------------------------------------------------------------------- # 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) = 0.32415005 grid = 40 40 72 stencil order = 5 estimated absolute RMS force accuracy = 0.0030008343 estimated relative force accuracy = 9.0369235e-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 1.00248 0.0764421 8304 2 97.302 11.741 2768 Per MPI rank memory allocation (min/avg/max) = 11.47 | 13.27 | 14.39 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 2923.2002 132115.2 0.91893312 428.55654 10.720085 96.541901 0 0 27273.876 69396.662 -315.17262 -271414.58 -174636.78 8088.7858 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.23417e-06 8304 2 103.7 9.37455e-05 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.34783e-06 8304 2 103.7 8.86293e-05 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.32238e-06 8304 2 103.7 0.000100457 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.32786e-06 8304 2 103.7 0.000101886 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.19092e-06 8304 2 103.7 0.00010019 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.32479e-06 8304 2 103.7 9.85416e-05 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.39152e-06 8304 2 103.7 0.000138529 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.18417e-06 8304 2 103.7 9.27476e-05 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.14212e-06 8304 2 103.7 9.35648e-05 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.38082e-06 8304 2 103.7 0.000108604 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.28877e-06 8304 2 103.7 9.37371e-05 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.49272e-06 8304 2 103.7 9.80716e-05 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.57543e-06 8304 2 103.7 0.000113582 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.24901e-06 8304 2 103.7 9.55032e-05 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.23007e-06 8304 2 103.7 9.07599e-05 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.24206e-06 8304 2 103.7 0.000110812 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.13183e-06 8304 2 103.7 8.74216e-05 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.45825e-06 8304 2 103.7 9.3882e-05 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.12154e-06 8304 2 103.7 8.90433e-05 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.39837e-06 8304 2 103.7 9.60976e-05 2768 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.46325e-06 8304 2 103.7 9.98197e-05 2768 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.08109e-06 8304 2 103.7 9.56148e-05 2768 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.1006e-06 8304 2 103.7 8.61752e-05 2768 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.39808e-06 8304 2 103.7 0.000104639 2768 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.20883e-06 8304 2 103.7 0.000100184 2768 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.43991e-06 8304 2 103.7 9.47602e-05 2768 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.83203e-06 8304 2 103.7 0.000134361 2768 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.40202e-06 8304 2 103.7 0.00012074 2768 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.23864e-06 8304 2 103.7 0.000110028 2768 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.06534e-06 8304 2 103.7 9.15276e-05 2768 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.16312e-06 8304 2 103.7 9.07403e-05 2768 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.26619e-06 8304 2 103.7 0.000103879 2768 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.8129e-06 8304 2 103.7 0.000119277 2768 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.12781e-06 8304 2 103.7 9.35646e-05 2768 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.16726e-06 8304 2 103.7 0.000109561 2768 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.30634e-06 8304 2 103.7 0.00010285 2768 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.06804e-06 8304 2 103.7 8.96018e-05 2768 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.41384e-06 8304 2 103.7 0.000111905 2768 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.09898e-06 8304 2 103.7 9.54278e-05 2768 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.60947e-06 8304 2 103.7 0.00012004 2768 SHAKE stats (type/ave/delta/count) on step 2050000 2 0.97 1.57982e-06 8304 2 103.7 0.000101346 2768 SHAKE stats (type/ave/delta/count) on step 2100000 2 0.97 1.20645e-06 8304 2 103.7 0.000100326 2768 SHAKE stats (type/ave/delta/count) on step 2150000 2 0.97 1.12469e-06 8304 2 103.7 9.55753e-05 2768 SHAKE stats (type/ave/delta/count) on step 2200000 2 0.97 1.35745e-06 8304 2 103.7 9.87201e-05 2768 SHAKE stats (type/ave/delta/count) on step 2250000 2 0.97 1.22594e-06 8304 2 103.7 9.66632e-05 2768 SHAKE stats (type/ave/delta/count) on step 2300000 2 0.97 1.22091e-06 8304 2 103.7 9.28514e-05 2768 SHAKE stats (type/ave/delta/count) on step 2350000 2 0.97 1.12713e-06 8304 2 103.7 8.99536e-05 2768 SHAKE stats (type/ave/delta/count) on step 2400000 2 0.97 1.32285e-06 8304 2 103.7 0.0001076 2768 SHAKE stats (type/ave/delta/count) on step 2450000 2 0.97 1.6772e-06 8304 2 103.7 0.000113388 2768 SHAKE stats (type/ave/delta/count) on step 2500000 2 0.97 1.41868e-06 8304 2 103.7 0.000109859 2768 SHAKE stats (type/ave/delta/count) on step 2550000 2 0.97 1.30348e-06 8304 2 103.7 9.04768e-05 2768 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.97 1.16592e-06 8304 2 103.7 9.13717e-05 2768 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.97 1.43204e-06 8304 2 103.7 0.000116565 2768 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.97 1.17735e-06 8304 2 103.7 0.000102459 2768 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.97 1.19318e-06 8304 2 103.7 9.5936e-05 2768 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.97 1.67831e-06 8304 2 103.7 0.000124419 2768 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.97 1.63848e-06 8304 2 103.7 0.000117399 2768 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.97 1.09971e-06 8304 2 103.7 0.000101737 2768 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.97 1.40404e-06 8304 2 103.7 0.000101659 2768 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.29572e-06 8304 2 103.7 0.000103086 2768 SHAKE stats (type/ave/delta/count) on step 3050000 2 0.97 1.22678e-06 8304 2 103.7 0.000101396 2768 SHAKE stats (type/ave/delta/count) on step 3100000 2 0.97 1.5115e-06 8304 2 103.7 0.000139542 2768 SHAKE stats (type/ave/delta/count) on step 3150000 2 0.97 1.28616e-06 8304 2 103.7 0.000101009 2768 SHAKE stats (type/ave/delta/count) on step 3200000 2 0.97 1.72762e-06 8304 2 103.7 0.000150968 2768 SHAKE stats (type/ave/delta/count) on step 3250000 2 0.97 1.3415e-06 8304 2 103.7 0.000103293 2768 SHAKE stats (type/ave/delta/count) on step 3300000 2 0.97 1.39128e-06 8304 2 103.7 0.0001188 2768 SHAKE stats (type/ave/delta/count) on step 3350000 2 0.97 1.1506e-06 8304 2 103.7 9.50363e-05 2768 SHAKE stats (type/ave/delta/count) on step 3400000 2 0.97 1.34099e-06 8304 2 103.7 0.00010362 2768 SHAKE stats (type/ave/delta/count) on step 3450000 2 0.97 1.15593e-06 8304 2 103.7 9.01935e-05 2768 SHAKE stats (type/ave/delta/count) on step 3500000 2 0.97 1.11737e-06 8304 2 103.7 9.51596e-05 2768 SHAKE stats (type/ave/delta/count) on step 3550000 2 0.97 1.23072e-06 8304 2 103.7 9.82702e-05 2768 SHAKE stats (type/ave/delta/count) on step 3600000 2 0.97 1.28687e-06 8304 2 103.7 0.000101398 2768 SHAKE stats (type/ave/delta/count) on step 3650000 2 0.97 1.04604e-06 8304 2 103.7 8.98167e-05 2768 SHAKE stats (type/ave/delta/count) on step 3700000 2 0.97 1.42941e-06 8304 2 103.7 0.000113105 2768 SHAKE stats (type/ave/delta/count) on step 3750000 2 0.97 1.44377e-06 8304 2 103.7 0.000100257 2768 SHAKE stats (type/ave/delta/count) on step 3800000 2 0.97 1.12216e-06 8304 2 103.7 9.40569e-05 2768 SHAKE stats (type/ave/delta/count) on step 3850000 2 0.97 1.43491e-06 8304 2 103.7 0.000112589 2768 SHAKE stats (type/ave/delta/count) on step 3900000 2 0.97 1.73748e-06 8304 2 103.7 0.000128783 2768 SHAKE stats (type/ave/delta/count) on step 3950000 2 0.97 1.07669e-06 8304 2 103.7 0.00010143 2768 SHAKE stats (type/ave/delta/count) on step 4000000 2 0.97 1.24978e-06 8304 2 103.7 0.000100173 2768 SHAKE stats (type/ave/delta/count) on step 4050000 2 0.97 1.13914e-06 8304 2 103.7 9.60982e-05 2768 SHAKE stats (type/ave/delta/count) on step 4100000 2 0.97 1.46999e-06 8304 2 103.7 9.64124e-05 2768 SHAKE stats (type/ave/delta/count) on step 4150000 2 0.97 1.3611e-06 8304 2 103.7 9.84844e-05 2768 SHAKE stats (type/ave/delta/count) on step 4200000 2 0.97 1.25108e-06 8304 2 103.7 9.79999e-05 2768 SHAKE stats (type/ave/delta/count) on step 4250000 2 0.97 1.18742e-06 8304 2 103.7 9.27927e-05 2768 SHAKE stats (type/ave/delta/count) on step 4300000 2 0.97 1.26432e-06 8304 2 103.7 8.78639e-05 2768 SHAKE stats (type/ave/delta/count) on step 4350000 2 0.97 1.12393e-06 8304 2 103.7 9.83425e-05 2768 SHAKE stats (type/ave/delta/count) on step 4400000 2 0.97 1.40388e-06 8304 2 103.7 9.06443e-05 2768 SHAKE stats (type/ave/delta/count) on step 4450000 2 0.97 1.58664e-06 8304 2 103.7 0.000119933 2768 SHAKE stats (type/ave/delta/count) on step 4500000 2 0.97 1.70264e-06 8304 2 103.7 0.00013349 2768 SHAKE stats (type/ave/delta/count) on step 4550000 2 0.97 1.34741e-06 8304 2 103.7 0.000109933 2768 SHAKE stats (type/ave/delta/count) on step 4600000 2 0.97 1.19574e-06 8304 2 103.7 8.93518e-05 2768 SHAKE stats (type/ave/delta/count) on step 4650000 2 0.97 2.18972e-06 8304 2 103.7 0.000139819 2768 SHAKE stats (type/ave/delta/count) on step 4700000 2 0.97 1.12316e-06 8304 2 103.7 9.30134e-05 2768 SHAKE stats (type/ave/delta/count) on step 4750000 2 0.97 1.31555e-06 8304 2 103.7 9.39657e-05 2768 SHAKE stats (type/ave/delta/count) on step 4800000 2 0.97 1.13933e-06 8304 2 103.7 9.32395e-05 2768 SHAKE stats (type/ave/delta/count) on step 4850000 2 0.97 1.10447e-06 8304 2 103.7 9.07913e-05 2768 SHAKE stats (type/ave/delta/count) on step 4900000 2 0.97 1.12798e-06 8304 2 103.7 9.03868e-05 2768 SHAKE stats (type/ave/delta/count) on step 4950000 2 0.97 1.41695e-06 8304 2 103.7 9.09545e-05 2768 SHAKE stats (type/ave/delta/count) on step 5000000 2 0.97 1.15189e-06 8304 2 103.7 9.9967e-05 2768 5000000 5000000 -223.66746 132115.2 0.91893312 295.95417 51.185693 87.279044 0 0 21051.633 89405.852 -315.17262 -271104.17 -160508.22 5585.9838 Loop time of 32717.1 on 32 procs for 5000000 steps with 9101 atoms Performance: 13.204 ns/day, 1.818 hours/ns, 152.825 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 | 93.954 | 10296 | 15361 |5400.2 | 31.47 Bond | 4.7878 | 12.878 | 29.154 | 175.0 | 0.04 Kspace | 12387 | 17486 | 27755 |4173.4 | 53.45 Neigh | 1306 | 1309.2 | 1316.1 | 8.9 | 4.00 Comm | 1044 | 1457.9 | 1631 | 592.2 | 4.46 Output | 0.012447 | 0.014725 | 0.016781 | 1.1 | 0.00 Modify | 1926.1 | 2064.9 | 2408.4 | 407.8 | 6.31 Other | | 90.24 | | | 0.28 Nlocal: 284.406 ave 410 max 0 min Histogram: 4 1 3 0 0 0 1 3 4 16 Nghost: 3963.66 ave 5307 max 2173 min Histogram: 8 0 4 0 3 1 0 1 3 12 Neighs: 76851.5 ave 126406 max 0 min Histogram: 4 2 2 4 0 0 0 2 16 2 Total # of neighbors = 2459249 Ave neighs/atom = 270.21745 Ave special neighs/atom = 1.8929788 Neighbor list builds = 249075 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) = 0.32415005 grid = 40 40 72 stencil order = 5 estimated absolute RMS force accuracy = 0.0030008343 estimated relative force accuracy = 9.0369235e-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 1.15189e-06 8304 2 103.7 9.9967e-05 2768 Per MPI rank memory allocation (min/avg/max) = 11.64 | 13.46 | 14.38 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 -222.98531 132115.2 0.91893312 295.95417 51.185693 87.279044 0 0 21051.633 89405.852 -315.17262 -271104.17 -160508.22 5585.9838 Loop time of 7.44738e-06 on 32 procs for 0 steps with 9101 atoms 117.5% 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 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 | | 7.447e-06 | | |100.00 Nlocal: 284.406 ave 410 max 0 min Histogram: 4 1 3 0 0 0 1 3 4 16 Nghost: 3963.66 ave 5307 max 2173 min Histogram: 8 0 4 0 3 1 0 1 3 12 Neighs: 76851.5 ave 126406 max 0 min Histogram: 4 2 2 4 0 0 0 2 16 2 Total # of neighbors = 2459249 Ave neighs/atom = 270.21745 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