#------------------------------------------------------------------------------- # Stage 2.4: NVT integration for 3 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 300000 300000 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 300 1 300 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 3000000 2.4.restart dump sci all custom 300000 2.4.xyz id mol type q xs ys zs timestep 1 run 3000000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.25049777 grid = 30 30 50 stencil order = 5 estimated absolute RMS force accuracy = 0.0035336797 estimated relative force accuracy = 1.0641571e-05 using double precision KISS FFT 3d grid and FFT values/proc = 6292 1800 generated 0 of 28 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.997525 0.63284 5784 2 98.2171 16.925 1928 Per MPI rank memory allocation (min/avg/max) = 10.93 | 12.22 | 13.52 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 -3735.8484 138406.7 0.6276451 427.16581 18.894135 36.807839 0 0 16135.052 4548.2801 -76.429471 -152164.91 -131425.87 5676.3721 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.29792e-06 5784 2 103.7 0.000107832 1928 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.01698e-06 5784 2 103.7 9.4205e-05 1928 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.35273e-06 5784 2 103.7 0.000108371 1928 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.11057e-06 5784 2 103.7 9.27783e-05 1928 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.38938e-06 5784 2 103.7 0.000108512 1928 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.32076e-06 5784 2 103.7 0.000105179 1928 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.19664e-06 5784 2 103.7 9.76351e-05 1928 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.23393e-06 5784 2 103.7 0.000123379 1928 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.25833e-06 5784 2 103.7 0.000123635 1928 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.0508e-06 5784 2 103.7 9.02752e-05 1928 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.67491e-06 5784 2 103.7 0.00013484 1928 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.37383e-06 5784 2 103.7 0.00010513 1928 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.04432e-06 5784 2 103.7 9.383e-05 1928 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.40898e-06 5784 2 103.7 0.000111039 1928 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.18803e-06 5784 2 103.7 8.67407e-05 1928 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.72437e-06 5784 2 103.7 0.000110821 1928 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.26878e-06 5784 2 103.7 9.56113e-05 1928 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.18638e-06 5784 2 103.7 9.55095e-05 1928 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.59073e-06 5784 2 103.7 0.000109682 1928 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.46793e-06 5784 2 103.7 0.000114512 1928 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.26286e-06 5784 2 103.7 9.53643e-05 1928 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.11362e-06 5784 2 103.7 9.81102e-05 1928 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.10278e-06 5784 2 103.7 9.29991e-05 1928 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.07687e-06 5784 2 103.7 9.623e-05 1928 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 2.09977e-06 5784 2 103.7 0.000110936 1928 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.17383e-06 5784 2 103.7 0.000126683 1928 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.1341e-06 5784 2 103.7 9.24531e-05 1928 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.67478e-06 5784 2 103.7 0.000110237 1928 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.12333e-06 5784 2 103.7 9.86073e-05 1928 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.23647e-06 5784 2 103.7 9.80129e-05 1928 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.27129e-06 5784 2 103.7 9.31362e-05 1928 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.16423e-06 5784 2 103.7 8.73178e-05 1928 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.3178e-06 5784 2 103.7 0.000139564 1928 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.29996e-06 5784 2 103.7 9.79915e-05 1928 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.27226e-06 5784 2 103.7 0.000115308 1928 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.47998e-06 5784 2 103.7 0.00010527 1928 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.02949e-06 5784 2 103.7 0.000100165 1928 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.21456e-06 5784 2 103.7 0.000109069 1928 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.14783e-06 5784 2 103.7 8.80196e-05 1928 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.1691e-06 5784 2 103.7 8.56817e-05 1928 SHAKE stats (type/ave/delta/count) on step 2050000 2 0.97 1.08897e-06 5784 2 103.7 8.94692e-05 1928 SHAKE stats (type/ave/delta/count) on step 2100000 2 0.97 1.49481e-06 5784 2 103.7 0.000100272 1928 SHAKE stats (type/ave/delta/count) on step 2150000 2 0.97 1.35265e-06 5784 2 103.7 9.98081e-05 1928 SHAKE stats (type/ave/delta/count) on step 2200000 2 0.97 1.3594e-06 5784 2 103.7 0.000102598 1928 SHAKE stats (type/ave/delta/count) on step 2250000 2 0.97 1.11676e-06 5784 2 103.7 9.28056e-05 1928 SHAKE stats (type/ave/delta/count) on step 2300000 2 0.97 1.0231e-06 5784 2 103.7 8.6432e-05 1928 SHAKE stats (type/ave/delta/count) on step 2350000 2 0.97 1.2967e-06 5784 2 103.7 9.34559e-05 1928 SHAKE stats (type/ave/delta/count) on step 2400000 2 0.97 1.33693e-06 5784 2 103.7 9.90255e-05 1928 SHAKE stats (type/ave/delta/count) on step 2450000 2 0.97 1.38048e-06 5784 2 103.7 0.000104582 1928 SHAKE stats (type/ave/delta/count) on step 2500000 2 0.97 1.63883e-06 5784 2 103.7 0.00012665 1928 SHAKE stats (type/ave/delta/count) on step 2550000 2 0.97 1.0156e-06 5784 2 103.7 9.11122e-05 1928 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.97 1.7785e-06 5784 2 103.7 0.000111325 1928 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.97 1.52997e-06 5784 2 103.7 0.000125297 1928 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.97 1.10225e-06 5784 2 103.7 8.65934e-05 1928 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.97 2.04414e-06 5784 2 103.7 0.000153074 1928 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.97 1.12653e-06 5784 2 103.7 9.01554e-05 1928 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.97 1.38659e-06 5784 2 103.7 0.000102722 1928 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.97 1.14755e-06 5784 2 103.7 9.60232e-05 1928 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.97 1.16033e-06 5784 2 103.7 9.41861e-05 1928 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.24717e-06 5784 2 103.7 8.8382e-05 1928 3000000 3000000 -138.38052 138406.7 0.6276451 297.01815 27.997386 32.187726 0 0 16300.985 11236.033 -76.429471 -152471.54 -124874.33 3946.9113 Loop time of 25600.4 on 32 procs for 3000000 steps with 6387 atoms Performance: 10.125 ns/day, 2.370 hours/ns, 117.186 timesteps/s 98.5% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.5676 | 7694.6 | 18274 |8441.1 | 30.06 Bond | 2.5633 | 5.5145 | 16.024 | 138.6 | 0.02 Kspace | 4070.3 | 14701 | 22562 |6149.9 | 57.42 Neigh | 1381.1 | 1386.9 | 1394.1 | 12.2 | 5.42 Comm | 224.49 | 641.05 | 891.41 | 928.4 | 2.50 Output | 0.012367 | 0.014244 | 0.015936 | 0.9 | 0.00 Modify | 937.85 | 1126.2 | 1371.7 | 513.7 | 4.40 Other | | 45.14 | | | 0.18 Nlocal: 199.594 ave 412 max 0 min Histogram: 12 0 0 0 3 5 0 0 0 12 Nghost: 3922.47 ave 7804 max 25 min Histogram: 4 0 8 0 2 6 0 8 0 4 Neighs: 91221.8 ave 223911 max 0 min Histogram: 12 4 0 2 2 0 0 0 8 4 Total # of neighbors = 2919099 Ave neighs/atom = 457.03758 Ave special neighs/atom = 1.8738062 Neighbor list builds = 145367 Dangerous builds = 0 undump sci restart 0 dump sci all custom 3000000 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) = 0.25049777 grid = 30 30 50 stencil order = 5 estimated absolute RMS force accuracy = 0.0035336797 estimated relative force accuracy = 1.0641571e-05 using double precision KISS FFT 3d grid and FFT values/proc = 6292 1800 generated 0 of 28 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.24717e-06 5784 2 103.7 8.8382e-05 1928 Per MPI rank memory allocation (min/avg/max) = 10.96 | 12.41 | 13.53 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 3000000 3000000 -137.95771 138406.7 0.6276451 297.01815 27.997386 32.187726 0 0 16300.985 11236.033 -76.429471 -152471.54 -124874.33 3946.9113 Loop time of 1.21118e-05 on 32 procs for 0 steps with 6387 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 | | 1.211e-05 | | |100.00 Nlocal: 199.594 ave 412 max 0 min Histogram: 12 0 0 0 3 5 0 0 0 12 Nghost: 3922.47 ave 7804 max 25 min Histogram: 4 0 8 0 2 6 0 8 0 4 Neighs: 91221.8 ave 223911 max 0 min Histogram: 12 4 0 2 2 0 0 0 8 4 Total # of neighbors = 2919099 Ave neighs/atom = 457.03758 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