#------------------------------------------------------------------------------- # 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) = 0.32021612 grid = 40 40 64 stencil order = 5 estimated absolute RMS force accuracy = 0.0032184304 estimated relative force accuracy = 9.6922075e-06 using double precision KISS FFT 3d grid and FFT values/proc = 10557 3200 generated 0 of 28 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.999948 0.631004 5784 2 97.8348 16.1811 1928 Per MPI rank memory allocation (min/avg/max) = 11.38 | 12.55 | 13.23 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 -1088.2388 136142.76 0.63808232 427.16581 9.5543792 16.51756 0 0 18042.175 43292.575 -154.3376 -194159.22 -132798.4 5676.3721 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.13499e-06 5784 2 103.7 8.92678e-05 1928 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.15539e-06 5784 2 103.7 0.000104896 1928 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.6001e-06 5784 2 103.7 0.000103493 1928 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.86232e-06 5784 2 103.7 0.000135253 1928 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.18246e-06 5784 2 103.7 8.93493e-05 1928 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.28125e-06 5784 2 103.7 0.000112158 1928 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.22714e-06 5784 2 103.7 0.000117449 1928 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.39245e-06 5784 2 103.7 0.00010457 1928 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.26807e-06 5784 2 103.7 0.000105856 1928 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.19218e-06 5784 2 103.7 8.97183e-05 1928 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.62601e-06 5784 2 103.7 0.000117311 1928 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.16755e-06 5784 2 103.7 0.000102063 1928 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.13301e-06 5784 2 103.7 8.61721e-05 1928 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.1158e-06 5784 2 103.7 8.99509e-05 1928 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.81037e-06 5784 2 103.7 0.000168261 1928 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.0766e-06 5784 2 103.7 9.50261e-05 1928 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.17939e-06 5784 2 103.7 9.09092e-05 1928 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.11649e-06 5784 2 103.7 9.42689e-05 1928 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.29911e-06 5784 2 103.7 8.95352e-05 1928 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.15745e-06 5784 2 103.7 8.69895e-05 1928 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.65383e-06 5784 2 103.7 0.000112931 1928 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.1572e-06 5784 2 103.7 9.94308e-05 1928 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.2291e-06 5784 2 103.7 0.000102268 1928 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.37081e-06 5784 2 103.7 9.72695e-05 1928 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.21284e-06 5784 2 103.7 9.32078e-05 1928 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.30152e-06 5784 2 103.7 0.000108227 1928 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.2646e-06 5784 2 103.7 9.28144e-05 1928 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.65766e-06 5784 2 103.7 0.000140333 1928 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.46468e-06 5784 2 103.7 0.000105741 1928 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.71622e-06 5784 2 103.7 0.000140136 1928 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.14269e-06 5784 2 103.7 0.000128003 1928 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.30285e-06 5784 2 103.7 9.95039e-05 1928 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.17367e-06 5784 2 103.7 0.000104006 1928 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.28446e-06 5784 2 103.7 0.000111514 1928 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.14898e-06 5784 2 103.7 8.86854e-05 1928 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.14991e-06 5784 2 103.7 0.000123461 1928 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.19655e-06 5784 2 103.7 9.42426e-05 1928 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.74085e-06 5784 2 103.7 0.000104898 1928 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.07999e-06 5784 2 103.7 0.000106444 1928 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.36313e-06 5784 2 103.7 0.000108589 1928 SHAKE stats (type/ave/delta/count) on step 2050000 2 0.97 1.13913e-06 5784 2 103.7 9.21906e-05 1928 SHAKE stats (type/ave/delta/count) on step 2100000 2 0.97 1.16009e-06 5784 2 103.7 9.52989e-05 1928 SHAKE stats (type/ave/delta/count) on step 2150000 2 0.97 1.16736e-06 5784 2 103.7 0.000109748 1928 SHAKE stats (type/ave/delta/count) on step 2200000 2 0.97 1.67639e-06 5784 2 103.7 0.000122352 1928 SHAKE stats (type/ave/delta/count) on step 2250000 2 0.97 1.24257e-06 5784 2 103.7 9.07688e-05 1928 SHAKE stats (type/ave/delta/count) on step 2300000 2 0.97 1.25877e-06 5784 2 103.7 0.000109178 1928 SHAKE stats (type/ave/delta/count) on step 2350000 2 0.97 1.69389e-06 5784 2 103.7 0.000112169 1928 SHAKE stats (type/ave/delta/count) on step 2400000 2 0.97 1.07148e-06 5784 2 103.7 9.39546e-05 1928 SHAKE stats (type/ave/delta/count) on step 2450000 2 0.97 1.14588e-06 5784 2 103.7 9.64244e-05 1928 SHAKE stats (type/ave/delta/count) on step 2500000 2 0.97 1.33661e-06 5784 2 103.7 0.000101593 1928 SHAKE stats (type/ave/delta/count) on step 2550000 2 0.97 1.30498e-06 5784 2 103.7 9.57046e-05 1928 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.97 1.12803e-06 5784 2 103.7 9.5965e-05 1928 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.97 1.24177e-06 5784 2 103.7 0.000122566 1928 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.97 1.18901e-06 5784 2 103.7 9.139e-05 1928 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.97 1.23811e-06 5784 2 103.7 9.66475e-05 1928 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.97 1.23284e-06 5784 2 103.7 0.000112472 1928 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.97 1.48409e-06 5784 2 103.7 0.000120694 1928 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.97 1.55251e-06 5784 2 103.7 8.77108e-05 1928 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.97 1.76164e-06 5784 2 103.7 0.000161317 1928 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.21546e-06 5784 2 103.7 9.04211e-05 1928 SHAKE stats (type/ave/delta/count) on step 3050000 2 0.97 1.19371e-06 5784 2 103.7 0.000100056 1928 SHAKE stats (type/ave/delta/count) on step 3100000 2 0.97 1.18322e-06 5784 2 103.7 0.000101551 1928 SHAKE stats (type/ave/delta/count) on step 3150000 2 0.97 1.1252e-06 5784 2 103.7 9.35616e-05 1928 SHAKE stats (type/ave/delta/count) on step 3200000 2 0.97 1.0561e-06 5784 2 103.7 9.15823e-05 1928 SHAKE stats (type/ave/delta/count) on step 3250000 2 0.97 1.17875e-06 5784 2 103.7 9.60374e-05 1928 SHAKE stats (type/ave/delta/count) on step 3300000 2 0.97 1.24543e-06 5784 2 103.7 8.95951e-05 1928 SHAKE stats (type/ave/delta/count) on step 3350000 2 0.97 1.18299e-06 5784 2 103.7 9.92194e-05 1928 SHAKE stats (type/ave/delta/count) on step 3400000 2 0.97 1.52558e-06 5784 2 103.7 0.000127074 1928 SHAKE stats (type/ave/delta/count) on step 3450000 2 0.97 1.31989e-06 5784 2 103.7 9.97664e-05 1928 SHAKE stats (type/ave/delta/count) on step 3500000 2 0.97 1.39854e-06 5784 2 103.7 0.000110963 1928 SHAKE stats (type/ave/delta/count) on step 3550000 2 0.97 1.33865e-06 5784 2 103.7 0.000104319 1928 SHAKE stats (type/ave/delta/count) on step 3600000 2 0.97 1.70432e-06 5784 2 103.7 0.000116983 1928 SHAKE stats (type/ave/delta/count) on step 3650000 2 0.97 1.19323e-06 5784 2 103.7 0.000100723 1928 SHAKE stats (type/ave/delta/count) on step 3700000 2 0.97 1.05201e-06 5784 2 103.7 0.000105934 1928 SHAKE stats (type/ave/delta/count) on step 3750000 2 0.97 1.19902e-06 5784 2 103.7 0.000103358 1928 SHAKE stats (type/ave/delta/count) on step 3800000 2 0.97 1.37599e-06 5784 2 103.7 9.20748e-05 1928 SHAKE stats (type/ave/delta/count) on step 3850000 2 0.97 1.32993e-06 5784 2 103.7 0.000111112 1928 SHAKE stats (type/ave/delta/count) on step 3900000 2 0.97 1.17492e-06 5784 2 103.7 9.47948e-05 1928 SHAKE stats (type/ave/delta/count) on step 3950000 2 0.97 1.25854e-06 5784 2 103.7 0.000100476 1928 SHAKE stats (type/ave/delta/count) on step 4000000 2 0.97 1.01928e-06 5784 2 103.7 9.88361e-05 1928 SHAKE stats (type/ave/delta/count) on step 4050000 2 0.97 1.26738e-06 5784 2 103.7 9.06466e-05 1928 SHAKE stats (type/ave/delta/count) on step 4100000 2 0.97 1.67453e-06 5784 2 103.7 0.000117118 1928 SHAKE stats (type/ave/delta/count) on step 4150000 2 0.97 1.18806e-06 5784 2 103.7 9.39546e-05 1928 SHAKE stats (type/ave/delta/count) on step 4200000 2 0.97 1.45568e-06 5784 2 103.7 0.000101931 1928 SHAKE stats (type/ave/delta/count) on step 4250000 2 0.97 1.28241e-06 5784 2 103.7 0.000105061 1928 SHAKE stats (type/ave/delta/count) on step 4300000 2 0.97 1.3895e-06 5784 2 103.7 9.83896e-05 1928 SHAKE stats (type/ave/delta/count) on step 4350000 2 0.97 1.2253e-06 5784 2 103.7 0.000100715 1928 SHAKE stats (type/ave/delta/count) on step 4400000 2 0.97 1.05788e-06 5784 2 103.7 9.38453e-05 1928 SHAKE stats (type/ave/delta/count) on step 4450000 2 0.97 1.07881e-06 5784 2 103.7 0.000102134 1928 SHAKE stats (type/ave/delta/count) on step 4500000 2 0.97 1.0823e-06 5784 2 103.7 0.000103178 1928 SHAKE stats (type/ave/delta/count) on step 4550000 2 0.97 1.12638e-06 5784 2 103.7 9.48674e-05 1928 SHAKE stats (type/ave/delta/count) on step 4600000 2 0.97 1.16336e-06 5784 2 103.7 8.73228e-05 1928 SHAKE stats (type/ave/delta/count) on step 4650000 2 0.97 1.0396e-06 5784 2 103.7 9.65941e-05 1928 SHAKE stats (type/ave/delta/count) on step 4700000 2 0.97 1.50473e-06 5784 2 103.7 9.36376e-05 1928 SHAKE stats (type/ave/delta/count) on step 4750000 2 0.97 1.51583e-06 5784 2 103.7 0.000111653 1928 SHAKE stats (type/ave/delta/count) on step 4800000 2 0.97 1.46394e-06 5784 2 103.7 0.000109338 1928 SHAKE stats (type/ave/delta/count) on step 4850000 2 0.97 1.13419e-06 5784 2 103.7 0.000114196 1928 SHAKE stats (type/ave/delta/count) on step 4900000 2 0.97 1.15588e-06 5784 2 103.7 9.53143e-05 1928 SHAKE stats (type/ave/delta/count) on step 4950000 2 0.97 1.52196e-06 5784 2 103.7 0.000127269 1928 SHAKE stats (type/ave/delta/count) on step 5000000 2 0.97 1.35686e-06 5784 2 103.7 0.000105442 1928 5000000 5000000 -85.724852 136142.76 0.63808232 298.28116 34.631655 42.388938 0 0 16338.57 53037.642 -154.3376 -194284.51 -124831.27 3963.6946 Loop time of 28003 on 32 procs for 5000000 steps with 6387 atoms Performance: 15.427 ns/day, 1.556 hours/ns, 178.553 timesteps/s 98.7% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 315.92 | 6889.2 | 14035 |7841.0 | 24.60 Bond | 4.4199 | 9.5447 | 24.955 | 179.3 | 0.03 Kspace | 10718 | 17932 | 24579 |4887.0 | 64.04 Neigh | 769.86 | 777.07 | 790.36 | 27.2 | 2.77 Comm | 564.58 | 867.83 | 1088.4 | 691.9 | 3.10 Output | 0.011426 | 0.013082 | 0.01466 | 0.9 | 0.00 Modify | 1293.9 | 1451.9 | 1667.3 | 407.7 | 5.18 Other | | 75.07 | | | 0.27 Nlocal: 199.594 ave 420 max 2 min Histogram: 14 2 0 0 0 0 0 1 5 10 Nghost: 2739.81 ave 4093 max 1437 min Histogram: 11 5 0 0 0 0 0 0 8 8 Neighs: 51558.7 ave 112354 max 370 min Histogram: 16 0 0 0 0 0 0 0 7 9 Total # of neighbors = 1649879 Ave neighs/atom = 258.3183 Ave special neighs/atom = 1.8738062 Neighbor list builds = 242396 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) = 0.32021612 grid = 40 40 64 stencil order = 5 estimated absolute RMS force accuracy = 0.0032184304 estimated relative force accuracy = 9.6922075e-06 using double precision KISS FFT 3d grid and FFT values/proc = 10557 3200 generated 0 of 28 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 5000000 2 0.97 1.35686e-06 5784 2 103.7 0.000105442 1928 Per MPI rank memory allocation (min/avg/max) = 12.49 | 12.86 | 13.23 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 -85.343695 136142.76 0.63808232 298.28116 34.631655 42.388938 0 0 16338.57 53037.642 -154.3376 -194284.51 -124831.27 3963.6946 Loop time of 7.05444e-06 on 32 procs for 0 steps with 6387 atoms 128.5% 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 | | 7.054e-06 | | |100.00 Nlocal: 199.594 ave 420 max 2 min Histogram: 14 2 0 0 0 0 0 1 5 10 Nghost: 2739.81 ave 4093 max 1437 min Histogram: 11 5 0 0 0 0 0 0 8 8 Neighs: 51558.7 ave 112354 max 370 min Histogram: 16 0 0 0 0 0 0 0 7 9 Total # of neighbors = 1649879 Ave neighs/atom = 258.3183 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