#------------------------------------------------------------------------------- # 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) = 0.31959374 grid = 40 40 64 stencil order = 5 estimated absolute RMS force accuracy = 0.0033035281 estimated relative force accuracy = 9.9484767e-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 0.998155 0.79511 5784 2 97.3217 31.8018 1928 Per MPI rank memory allocation (min/avg/max) = 11.37 | 12.51 | 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-06 470.13544 138878.58 0.6255125 427.16581 25.801395 164.0631 0 0 16999.589 48425.055 -151.29725 -192582.1 -126967.6 5676.3721 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.32857e-06 5784 2 103.7 8.80302e-05 1928 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.41418e-06 5784 2 103.7 9.52401e-05 1928 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.49388e-06 5784 2 103.7 0.000101271 1928 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.04919e-06 5784 2 103.7 9.92253e-05 1928 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.32861e-06 5784 2 103.7 0.000103008 1928 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.54827e-06 5784 2 103.7 0.000111928 1928 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.30077e-06 5784 2 103.7 0.000100194 1928 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.03585e-06 5784 2 103.7 9.6417e-05 1928 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.45743e-06 5784 2 103.7 0.000125482 1928 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.31105e-06 5784 2 103.7 9.10348e-05 1928 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.27538e-06 5784 2 103.7 8.88963e-05 1928 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.4122e-06 5784 2 103.7 0.000104076 1928 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.49767e-06 5784 2 103.7 0.0001075 1928 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.43062e-06 5784 2 103.7 0.000113286 1928 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.29143e-06 5784 2 103.7 9.4019e-05 1928 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.36925e-06 5784 2 103.7 9.85047e-05 1928 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.17085e-06 5784 2 103.7 0.000100048 1928 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.16315e-06 5784 2 103.7 9.4302e-05 1928 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.08647e-06 5784 2 103.7 9.49714e-05 1928 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.18083e-06 5784 2 103.7 8.94684e-05 1928 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.45806e-06 5784 2 103.7 0.000117168 1928 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.26052e-06 5784 2 103.7 9.58499e-05 1928 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.34763e-06 5784 2 103.7 0.000107858 1928 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.29677e-06 5784 2 103.7 9.4026e-05 1928 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.33359e-06 5784 2 103.7 9.82602e-05 1928 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.23522e-06 5784 2 103.7 9.85162e-05 1928 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.16709e-06 5784 2 103.7 9.79852e-05 1928 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.10131e-06 5784 2 103.7 9.01142e-05 1928 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.02124e-06 5784 2 103.7 8.91317e-05 1928 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.14341e-06 5784 2 103.7 8.98328e-05 1928 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.08523e-06 5784 2 103.7 9.78957e-05 1928 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.20852e-06 5784 2 103.7 9.22555e-05 1928 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.47378e-06 5784 2 103.7 9.22232e-05 1928 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.21294e-06 5784 2 103.7 9.56093e-05 1928 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.14499e-06 5784 2 103.7 8.97122e-05 1928 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.47168e-06 5784 2 103.7 9.93917e-05 1928 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.8584e-06 5784 2 103.7 0.000103993 1928 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.50194e-06 5784 2 103.7 0.000103279 1928 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.08949e-06 5784 2 103.7 9.47433e-05 1928 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.26314e-06 5784 2 103.7 9.39986e-05 1928 SHAKE stats (type/ave/delta/count) on step 2050000 2 0.97 9.28952e-07 5784 2 103.7 9.51589e-05 1928 SHAKE stats (type/ave/delta/count) on step 2100000 2 0.97 1.12944e-06 5784 2 103.7 0.000104862 1928 SHAKE stats (type/ave/delta/count) on step 2150000 2 0.97 1.19466e-06 5784 2 103.7 9.50128e-05 1928 SHAKE stats (type/ave/delta/count) on step 2200000 2 0.97 1.09895e-06 5784 2 103.7 9.67993e-05 1928 SHAKE stats (type/ave/delta/count) on step 2250000 2 0.97 1.57253e-06 5784 2 103.7 0.000106526 1928 SHAKE stats (type/ave/delta/count) on step 2300000 2 0.97 1.04182e-06 5784 2 103.7 9.26066e-05 1928 SHAKE stats (type/ave/delta/count) on step 2350000 2 0.97 1.54557e-06 5784 2 103.7 0.000117603 1928 SHAKE stats (type/ave/delta/count) on step 2400000 2 0.97 1.06341e-06 5784 2 103.7 9.06305e-05 1928 SHAKE stats (type/ave/delta/count) on step 2450000 2 0.97 1.21565e-06 5784 2 103.7 0.000104408 1928 SHAKE stats (type/ave/delta/count) on step 2500000 2 0.97 1.24895e-06 5784 2 103.7 9.28651e-05 1928 SHAKE stats (type/ave/delta/count) on step 2550000 2 0.97 1.15733e-06 5784 2 103.7 8.87036e-05 1928 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.97 1.26791e-06 5784 2 103.7 9.63187e-05 1928 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.97 1.17224e-06 5784 2 103.7 8.94123e-05 1928 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.97 1.64284e-06 5784 2 103.7 0.000141619 1928 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.97 1.07215e-06 5784 2 103.7 8.69236e-05 1928 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.97 1.80818e-06 5784 2 103.7 0.00013993 1928 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.97 1.52178e-06 5784 2 103.7 0.000117734 1928 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.97 1.29925e-06 5784 2 103.7 9.2513e-05 1928 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.97 1.14506e-06 5784 2 103.7 0.000107865 1928 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.19727e-06 5784 2 103.7 9.21797e-05 1928 SHAKE stats (type/ave/delta/count) on step 3050000 2 0.97 1.24374e-06 5784 2 103.7 0.000100972 1928 SHAKE stats (type/ave/delta/count) on step 3100000 2 0.97 1.10196e-06 5784 2 103.7 8.67844e-05 1928 SHAKE stats (type/ave/delta/count) on step 3150000 2 0.97 1.54966e-06 5784 2 103.7 0.000108086 1928 SHAKE stats (type/ave/delta/count) on step 3200000 2 0.97 1.04379e-06 5784 2 103.7 9.18241e-05 1928 SHAKE stats (type/ave/delta/count) on step 3250000 2 0.97 1.38612e-06 5784 2 103.7 9.63177e-05 1928 SHAKE stats (type/ave/delta/count) on step 3300000 2 0.97 1.05106e-06 5784 2 103.7 9.0429e-05 1928 SHAKE stats (type/ave/delta/count) on step 3350000 2 0.97 1.41602e-06 5784 2 103.7 0.000110151 1928 SHAKE stats (type/ave/delta/count) on step 3400000 2 0.97 1.14481e-06 5784 2 103.7 0.000101999 1928 SHAKE stats (type/ave/delta/count) on step 3450000 2 0.97 1.07709e-06 5784 2 103.7 0.000104909 1928 SHAKE stats (type/ave/delta/count) on step 3500000 2 0.97 1.20071e-06 5784 2 103.7 0.000105408 1928 SHAKE stats (type/ave/delta/count) on step 3550000 2 0.97 1.47874e-06 5784 2 103.7 0.000110696 1928 SHAKE stats (type/ave/delta/count) on step 3600000 2 0.97 1.16926e-06 5784 2 103.7 0.000114538 1928 SHAKE stats (type/ave/delta/count) on step 3650000 2 0.97 1.08728e-06 5784 2 103.7 8.94155e-05 1928 SHAKE stats (type/ave/delta/count) on step 3700000 2 0.97 1.57635e-06 5784 2 103.7 0.000112056 1928 SHAKE stats (type/ave/delta/count) on step 3750000 2 0.97 1.44204e-06 5784 2 103.7 9.8696e-05 1928 SHAKE stats (type/ave/delta/count) on step 3800000 2 0.97 1.23072e-06 5784 2 103.7 0.000119605 1928 SHAKE stats (type/ave/delta/count) on step 3850000 2 0.97 1.50352e-06 5784 2 103.7 9.31157e-05 1928 SHAKE stats (type/ave/delta/count) on step 3900000 2 0.97 1.28448e-06 5784 2 103.7 9.26219e-05 1928 SHAKE stats (type/ave/delta/count) on step 3950000 2 0.97 1.15622e-06 5784 2 103.7 8.80317e-05 1928 SHAKE stats (type/ave/delta/count) on step 4000000 2 0.97 1.32363e-06 5784 2 103.7 0.0001086 1928 SHAKE stats (type/ave/delta/count) on step 4050000 2 0.97 1.31991e-06 5784 2 103.7 9.74689e-05 1928 SHAKE stats (type/ave/delta/count) on step 4100000 2 0.97 1.19154e-06 5784 2 103.7 9.61872e-05 1928 SHAKE stats (type/ave/delta/count) on step 4150000 2 0.97 1.21479e-06 5784 2 103.7 9.99165e-05 1928 SHAKE stats (type/ave/delta/count) on step 4200000 2 0.97 1.63623e-06 5784 2 103.7 0.000117464 1928 SHAKE stats (type/ave/delta/count) on step 4250000 2 0.97 1.47014e-06 5784 2 103.7 0.00010755 1928 SHAKE stats (type/ave/delta/count) on step 4300000 2 0.97 1.06764e-06 5784 2 103.7 8.92791e-05 1928 SHAKE stats (type/ave/delta/count) on step 4350000 2 0.97 1.06263e-06 5784 2 103.7 0.000104853 1928 SHAKE stats (type/ave/delta/count) on step 4400000 2 0.97 1.72676e-06 5784 2 103.7 0.000117845 1928 SHAKE stats (type/ave/delta/count) on step 4450000 2 0.97 9.91026e-07 5784 2 103.7 9.29561e-05 1928 SHAKE stats (type/ave/delta/count) on step 4500000 2 0.97 1.45761e-06 5784 2 103.7 0.000112291 1928 SHAKE stats (type/ave/delta/count) on step 4550000 2 0.97 1.12638e-06 5784 2 103.7 9.97972e-05 1928 SHAKE stats (type/ave/delta/count) on step 4600000 2 0.97 1.26297e-06 5784 2 103.7 9.32357e-05 1928 SHAKE stats (type/ave/delta/count) on step 4650000 2 0.97 1.07407e-06 5784 2 103.7 0.000110875 1928 SHAKE stats (type/ave/delta/count) on step 4700000 2 0.97 1.12355e-06 5784 2 103.7 0.000119292 1928 SHAKE stats (type/ave/delta/count) on step 4750000 2 0.97 9.84192e-07 5784 2 103.7 9.83776e-05 1928 SHAKE stats (type/ave/delta/count) on step 4800000 2 0.97 1.32086e-06 5784 2 103.7 0.00013027 1928 SHAKE stats (type/ave/delta/count) on step 4850000 2 0.97 1.02073e-06 5784 2 103.7 9.69149e-05 1928 SHAKE stats (type/ave/delta/count) on step 4900000 2 0.97 2.04189e-06 5784 2 103.7 0.000165334 1928 SHAKE stats (type/ave/delta/count) on step 4950000 2 0.97 1.23663e-06 5784 2 103.7 0.000133787 1928 SHAKE stats (type/ave/delta/count) on step 5000000 2 0.97 1.12188e-06 5784 2 103.7 0.000109097 1928 5000000 5000000 -167.1201 138878.58 0.6255125 295.5991 34.184209 41.390978 0 0 16336.753 52515.396 -151.29725 -193856.02 -124928.3 3928.0542 Loop time of 29042.6 on 32 procs for 5000000 steps with 6387 atoms Performance: 14.875 ns/day, 1.613 hours/ns, 172.161 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 | 150.61 | 6901.6 | 15038 |7992.6 | 23.76 Bond | 4.2848 | 9.699 | 28.167 | 197.5 | 0.03 Kspace | 10740 | 18945 | 25771 |4852.1 | 65.23 Neigh | 790.09 | 797.48 | 810.92 | 27.7 | 2.75 Comm | 520.33 | 843.79 | 1072.2 | 727.5 | 2.91 Output | 0.012324 | 0.013946 | 0.015533 | 0.8 | 0.00 Modify | 1309.1 | 1469.3 | 1690.8 | 408.6 | 5.06 Other | | 75.51 | | | 0.26 Nlocal: 199.594 ave 414 max 0 min Histogram: 13 3 0 0 0 0 0 0 7 9 Nghost: 2699.28 ave 4118 max 1317 min Histogram: 8 8 0 0 0 0 0 0 8 8 Neighs: 51250.6 ave 111303 max 0 min Histogram: 16 0 0 0 0 0 0 0 5 11 Total # of neighbors = 1640019 Ave neighs/atom = 256.77454 Ave special neighs/atom = 1.8738062 Neighbor list builds = 241833 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) = 0.31959374 grid = 40 40 64 stencil order = 5 estimated absolute RMS force accuracy = 0.0033035281 estimated relative force accuracy = 9.9484767e-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 1.12188e-06 5784 2 103.7 0.000109097 1928 Per MPI rank memory allocation (min/avg/max) = 11.5 | 12.73 | 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 -166.61203 138878.58 0.6255125 295.5991 34.184209 41.390978 0 0 16336.753 52515.396 -151.29725 -193856.02 -124928.3 3928.0542 Loop time of 8.45269e-06 on 32 procs for 0 steps with 6387 atoms 112.0% 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 | | 8.453e-06 | | |100.00 Nlocal: 199.594 ave 414 max 0 min Histogram: 13 3 0 0 0 0 0 0 7 9 Nghost: 2699.28 ave 4118 max 1317 min Histogram: 8 8 0 0 0 0 0 0 8 8 Neighs: 51250.6 ave 111303 max 0 min Histogram: 16 0 0 0 0 0 0 0 5 11 Total # of neighbors = 1640019 Ave neighs/atom = 256.77454 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