#------------------------------------------------------------------------------- # 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 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 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) = 0.32729257 grid = 40 40 40 stencil order = 5 estimated absolute RMS force accuracy = 0.0030709373 estimated relative force accuracy = 9.2480364e-06 using double precision KISS FFT 3d grid and FFT values/proc = 7803 3200 generated 0 of 28 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.996827 0.68327 5784 2 96.73 33.4302 1928 Per MPI rank memory allocation (min/avg/max) = 12.42 | 12.54 | 12.73 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 15634.301 65360.011 1.3291045 427.16581 53.256516 145.3355 0 0 19056.64 63828.305 -321.48015 -196920.52 -113836.99 5676.3721 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.15861e-06 5784 2 103.7 9.99358e-05 1928 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.71408e-06 5784 2 103.7 0.000161765 1928 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.76599e-06 5784 2 103.7 0.000109769 1928 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.34842e-06 5784 2 103.7 0.000106889 1928 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.06698e-06 5784 2 103.7 0.000101466 1928 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.20774e-06 5784 2 103.7 0.000119207 1928 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.20692e-06 5784 2 103.7 9.8141e-05 1928 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.07337e-06 5784 2 103.7 8.83589e-05 1928 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.15146e-06 5784 2 103.7 0.000112632 1928 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.29275e-06 5784 2 103.7 9.84294e-05 1928 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.15317e-06 5784 2 103.7 9.29649e-05 1928 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.19009e-06 5784 2 103.7 9.33464e-05 1928 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.04723e-06 5784 2 103.7 9.64847e-05 1928 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.29722e-06 5784 2 103.7 8.96135e-05 1928 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.3945e-06 5784 2 103.7 9.22847e-05 1928 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.13225e-06 5784 2 103.7 9.15613e-05 1928 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.12581e-06 5784 2 103.7 9.41173e-05 1928 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.5534e-06 5784 2 103.7 0.000114723 1928 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.26265e-06 5784 2 103.7 0.000112577 1928 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.09807e-06 5784 2 103.7 9.02216e-05 1928 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.03635e-06 5784 2 103.7 9.37925e-05 1928 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.25003e-06 5784 2 103.7 9.93628e-05 1928 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.18149e-06 5784 2 103.7 0.000101338 1928 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.07787e-06 5784 2 103.7 0.000106055 1928 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.23864e-06 5784 2 103.7 9.58335e-05 1928 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 2.11239e-06 5784 2 103.7 0.000126979 1928 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.37468e-06 5784 2 103.7 0.000104935 1928 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.33317e-06 5784 2 103.7 8.68471e-05 1928 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.42192e-06 5784 2 103.7 9.12382e-05 1928 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.2404e-06 5784 2 103.7 9.94769e-05 1928 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.15269e-06 5784 2 103.7 9.97727e-05 1928 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.11687e-06 5784 2 103.7 0.000102084 1928 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.22155e-06 5784 2 103.7 9.71893e-05 1928 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.67977e-06 5784 2 103.7 0.000108931 1928 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.41585e-06 5784 2 103.7 8.93491e-05 1928 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.59687e-06 5784 2 103.7 9.76779e-05 1928 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.22434e-06 5784 2 103.7 9.79634e-05 1928 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.18102e-06 5784 2 103.7 9.69714e-05 1928 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.10748e-06 5784 2 103.7 0.000104861 1928 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.13036e-06 5784 2 103.7 9.35193e-05 1928 2000000 2000000 2787.0284 65360.011 1.3291045 304.39203 29.366107 35.462154 0 0 17244.339 55273.617 -321.48015 -198542.18 -125959.39 4044.8986 Loop time of 8175.19 on 32 procs for 2000000 steps with 6387 atoms Performance: 21.137 ns/day, 1.135 hours/ns, 244.643 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 | 3160.1 | 3415 | 3764.4 | 243.9 | 41.77 Bond | 1.9074 | 3.9908 | 9.3299 | 96.4 | 0.05 Kspace | 3006.2 | 3354.1 | 3607.5 | 247.1 | 41.03 Neigh | 196.02 | 196.51 | 196.96 | 2.3 | 2.40 Comm | 576.33 | 586.04 | 593.23 | 14.7 | 7.17 Output | 0.0088717 | 0.010768 | 0.012544 | 1.1 | 0.00 Modify | 586.99 | 591.18 | 598.23 | 11.4 | 7.23 Other | | 28.35 | | | 0.35 Nlocal: 199.594 ave 215 max 185 min Histogram: 3 3 3 4 1 4 6 3 3 2 Nghost: 4407.62 ave 4450 max 4363 min Histogram: 2 1 3 3 7 5 5 3 2 1 Neighs: 62000.2 ave 69566 max 55801 min Histogram: 4 2 5 4 1 6 4 4 1 1 Total # of neighbors = 1984006 Ave neighs/atom = 310.63191 Ave special neighs/atom = 1.8738062 Neighbor list builds = 94973 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) = 0.32729257 grid = 40 40 40 stencil order = 5 estimated absolute RMS force accuracy = 0.0030709373 estimated relative force accuracy = 9.2480364e-06 using double precision KISS FFT 3d grid and FFT values/proc = 7803 3200 generated 0 of 28 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.13036e-06 5784 2 103.7 9.35193e-05 1928 Per MPI rank memory allocation (min/avg/max) = 12.42 | 12.59 | 12.73 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 2788.0845 65360.011 1.3291045 304.39203 29.366107 35.462154 0 0 17244.339 55273.617 -321.48015 -198542.18 -125959.39 4044.8986 Loop time of 7.93441e-06 on 32 procs for 0 steps with 6387 atoms 115.0% 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 | | 7.934e-06 | | |100.00 Nlocal: 199.594 ave 215 max 185 min Histogram: 3 3 3 4 1 4 6 3 3 2 Nghost: 4407.62 ave 4450 max 4363 min Histogram: 2 1 3 3 7 5 5 3 2 1 Neighs: 62000.2 ave 69566 max 55801 min Histogram: 4 2 5 4 1 6 4 4 1 1 Total # of neighbors = 1984006 Ave neighs/atom = 310.63191 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_NPT.out