#------------------------------------------------------------------------------- # Stage 2.4: NVT integration for 2 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 200000 200000 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 200 1 200 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 2000000 2.4.restart dump sci all custom 200000 2.4.xyz id mol type q xs ys zs timestep 1 run 2000000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.32734069 grid = 45 45 45 stencil order = 5 estimated absolute RMS force accuracy = 0.0029667961 estimated relative force accuracy = 8.9344182e-06 using double precision KISS FFT 3d grid and FFT values/proc = 9396 4050 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.994387 0.703974 8304 2 97.4104 23.2752 2768 Per MPI rank memory allocation (min/avg/max) = 12.63 | 12.84 | 13.22 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 8828.9298 92859.489 1.3074058 428.55654 109.80162 220.88661 0 0 23523.134 93391.742 -448.40969 -272779.85 -155534.29 8088.7858 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.23455e-06 8304 2 103.7 0.000114895 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.37313e-06 8304 2 103.7 9.38675e-05 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.21884e-06 8304 2 103.7 0.000103874 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.3532e-06 8304 2 103.7 9.05463e-05 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.06178e-06 8304 2 103.7 9.59837e-05 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.11499e-06 8304 2 103.7 0.00010025 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.9313e-06 8304 2 103.7 0.00012983 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.75518e-06 8304 2 103.7 0.000143287 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.1488e-06 8304 2 103.7 9.45754e-05 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.22449e-06 8304 2 103.7 9.75252e-05 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.38599e-06 8304 2 103.7 9.98748e-05 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.52234e-06 8304 2 103.7 0.000101789 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.49576e-06 8304 2 103.7 8.93806e-05 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.24104e-06 8304 2 103.7 9.54291e-05 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.16857e-06 8304 2 103.7 8.80463e-05 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.35952e-06 8304 2 103.7 8.9707e-05 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.11942e-06 8304 2 103.7 9.0854e-05 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.29938e-06 8304 2 103.7 0.000105687 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.24933e-06 8304 2 103.7 9.15998e-05 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.13123e-06 8304 2 103.7 8.83805e-05 2768 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.42998e-06 8304 2 103.7 9.75918e-05 2768 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.18324e-06 8304 2 103.7 8.81348e-05 2768 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.28684e-06 8304 2 103.7 9.20853e-05 2768 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.23023e-06 8304 2 103.7 9.49001e-05 2768 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.25731e-06 8304 2 103.7 0.000107011 2768 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.19556e-06 8304 2 103.7 0.000122653 2768 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.24136e-06 8304 2 103.7 9.30687e-05 2768 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.53667e-06 8304 2 103.7 0.00012825 2768 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.28913e-06 8304 2 103.7 9.33853e-05 2768 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.42704e-06 8304 2 103.7 9.05352e-05 2768 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.22762e-06 8304 2 103.7 0.000115246 2768 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.389e-06 8304 2 103.7 0.000100458 2768 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.37393e-06 8304 2 103.7 9.66679e-05 2768 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.62291e-06 8304 2 103.7 0.000103479 2768 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.19474e-06 8304 2 103.7 9.39042e-05 2768 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.52762e-06 8304 2 103.7 0.000100716 2768 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.57926e-06 8304 2 103.7 9.77565e-05 2768 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.76006e-06 8304 2 103.7 0.000121279 2768 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.14165e-06 8304 2 103.7 9.58193e-05 2768 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.26994e-06 8304 2 103.7 9.09769e-05 2768 2000000 2000000 2577.7447 92859.489 1.3074058 294.98121 49.533279 62.375248 0 0 22308.023 89590.918 -448.40969 -273804.51 -161793.66 5567.6197 Loop time of 11443.2 on 32 procs for 2000000 steps with 9101 atoms Performance: 15.101 ns/day, 1.589 hours/ns, 174.776 timesteps/s 99.3% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4489.3 | 4820.3 | 5306.8 | 279.7 | 42.12 Bond | 2.3213 | 5.3878 | 11.19 | 98.3 | 0.05 Kspace | 4212.6 | 4700.8 | 5035.9 | 283.2 | 41.08 Neigh | 320.28 | 321.34 | 322.12 | 3.1 | 2.81 Comm | 724.33 | 732.55 | 742.32 | 18.8 | 6.40 Output | 0.012484 | 0.014752 | 0.016897 | 1.1 | 0.00 Modify | 820.74 | 825.14 | 829.85 | 8.7 | 7.21 Other | | 37.64 | | | 0.33 Nlocal: 284.406 ave 307 max 265 min Histogram: 2 1 5 4 5 9 2 1 2 1 Nghost: 4984.81 ave 5031 max 4933 min Histogram: 2 2 2 3 5 5 4 4 3 2 Neighs: 88644.5 ave 95454 max 76952 min Histogram: 2 0 0 3 1 5 7 6 5 3 Total # of neighbors = 2836625 Ave neighs/atom = 311.68278 Ave special neighs/atom = 1.8929788 Neighbor list builds = 98278 Dangerous builds = 0 undump sci restart 0 dump sci all custom 2000000 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) = 0.32734069 grid = 45 45 45 stencil order = 5 estimated absolute RMS force accuracy = 0.0029667961 estimated relative force accuracy = 8.9344182e-06 using double precision KISS FFT 3d grid and FFT values/proc = 9396 4050 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.26994e-06 8304 2 103.7 9.09769e-05 2768 Per MPI rank memory allocation (min/avg/max) = 12.64 | 13.09 | 13.34 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 2000000 2000000 2578.7144 92859.489 1.3074058 294.98121 49.533279 62.375248 0 0 22308.023 89590.918 -448.40969 -273804.51 -161793.66 5567.6197 Loop time of 7.72384e-06 on 32 procs for 0 steps with 9101 atoms 109.6% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 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 | | 7.724e-06 | | |100.00 Nlocal: 284.406 ave 307 max 265 min Histogram: 2 1 5 4 5 9 2 1 2 1 Nghost: 4984.81 ave 5031 max 4933 min Histogram: 2 2 2 3 5 5 4 4 3 2 Neighs: 88644.5 ave 95454 max 76952 min Histogram: 2 0 0 3 1 5 7 6 5 3 Total # of neighbors = 2836625 Ave neighs/atom = 311.68278 Ave special neighs/atom = 1.8929788 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken log 2.5_NPT.out