#------------------------------------------------------------------------------- # 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) = 0.25979226 grid = 36 36 36 stencil order = 5 estimated absolute RMS force accuracy = 0.0025175327 estimated relative force accuracy = 7.5814749e-06 using double precision KISS FFT 3d grid and FFT values/proc = 6400 2592 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.99391 0.898052 8304 2 97.1518 38.2601 2768 Per MPI rank memory allocation (min/avg/max) = 12.9 | 13 | 13.58 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 16871.438 92859.489 1.3074058 428.55654 332.00115 402.77997 0 0 25466.176 47997.897 -225.64505 -216735.61 -142536.76 8088.7858 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.54442e-06 8304 2 103.7 9.95583e-05 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.24727e-06 8304 2 103.7 0.00010125 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.31735e-06 8304 2 103.7 0.000105182 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.09171e-06 8304 2 103.7 0.000102151 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.06056e-06 8304 2 103.7 9.15084e-05 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.15642e-06 8304 2 103.7 9.1805e-05 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.29863e-06 8304 2 103.7 0.00010035 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.09696e-06 8304 2 103.7 9.04142e-05 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.52169e-06 8304 2 103.7 9.96557e-05 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.18065e-06 8304 2 103.7 9.93137e-05 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.19055e-06 8304 2 103.7 9.17401e-05 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.20541e-06 8304 2 103.7 0.000112947 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.73009e-06 8304 2 103.7 0.000134296 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.21362e-06 8304 2 103.7 9.89654e-05 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.17242e-06 8304 2 103.7 9.76719e-05 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.2276e-06 8304 2 103.7 9.78029e-05 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.07346e-06 8304 2 103.7 9.56204e-05 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.08827e-06 8304 2 103.7 9.38347e-05 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.17063e-06 8304 2 103.7 9.30561e-05 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.36833e-06 8304 2 103.7 9.35006e-05 2768 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.05877e-06 8304 2 103.7 0.000100294 2768 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.09989e-06 8304 2 103.7 9.09914e-05 2768 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.36127e-06 8304 2 103.7 9.72732e-05 2768 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.20615e-06 8304 2 103.7 0.000102551 2768 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.28161e-06 8304 2 103.7 0.000101716 2768 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.60244e-06 8304 2 103.7 0.000104678 2768 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.15907e-06 8304 2 103.7 0.000101097 2768 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.44353e-06 8304 2 103.7 0.000116603 2768 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.20502e-06 8304 2 103.7 8.75581e-05 2768 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.72129e-06 8304 2 103.7 0.00010017 2768 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.16232e-06 8304 2 103.7 9.90664e-05 2768 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.71373e-06 8304 2 103.7 0.000124456 2768 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.28028e-06 8304 2 103.7 0.000110372 2768 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.48933e-06 8304 2 103.7 0.000107751 2768 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.20011e-06 8304 2 103.7 8.97906e-05 2768 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.35934e-06 8304 2 103.7 0.00010093 2768 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.62877e-06 8304 2 103.7 0.000101567 2768 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.52557e-06 8304 2 103.7 0.000105751 2768 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.13335e-06 8304 2 103.7 9.59672e-05 2768 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.34114e-06 8304 2 103.7 9.83526e-05 2768 2000000 2000000 2309.2288 92859.489 1.3074058 300.56167 42.687475 59.823023 0 0 21930.049 34465.429 -225.64505 -218033.74 -161535.76 5672.948 Loop time of 15550.9 on 32 procs for 2000000 steps with 9101 atoms Performance: 11.112 ns/day, 2.160 hours/ns, 128.610 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 | 8068.7 | 8978.6 | 9882.3 | 606.3 | 57.74 Bond | 2.4701 | 5.6642 | 11.592 | 85.0 | 0.04 Kspace | 3040.8 | 3948.9 | 4845.7 | 911.5 | 25.39 Neigh | 499.2 | 499.93 | 500.9 | 2.5 | 3.21 Comm | 1041.8 | 1060.4 | 1077.4 | 30.7 | 6.82 Output | 0.012259 | 0.014513 | 0.016594 | 1.1 | 0.00 Modify | 1003.1 | 1009.4 | 1021.2 | 14.4 | 6.49 Other | | 47.87 | | | 0.31 Nlocal: 284.406 ave 302 max 262 min Histogram: 2 3 2 0 3 9 2 4 1 6 Nghost: 7390.47 ave 7474 max 7302 min Histogram: 2 0 5 5 3 5 3 4 3 2 Neighs: 160113 ave 183769 max 133544 min Histogram: 1 4 4 2 4 3 4 3 3 4 Total # of neighbors = 5123615 Ave neighs/atom = 562.97275 Ave special neighs/atom = 1.8929788 Neighbor list builds = 98373 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) = 0.25979226 grid = 36 36 36 stencil order = 5 estimated absolute RMS force accuracy = 0.0025175327 estimated relative force accuracy = 7.5814749e-06 using double precision KISS FFT 3d grid and FFT values/proc = 6400 2592 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.34114e-06 8304 2 103.7 9.83526e-05 2768 Per MPI rank memory allocation (min/avg/max) = 12.9 | 13.13 | 13.59 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 2310.0978 92859.489 1.3074058 300.56167 42.687475 59.823023 0 0 21930.049 34465.429 -225.64505 -218033.74 -161535.76 5672.948 Loop time of 8.37638e-06 on 32 procs for 0 steps with 9101 atoms 107.4% 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 | | 8.376e-06 | | |100.00 Nlocal: 284.406 ave 302 max 262 min Histogram: 2 3 2 0 3 9 2 4 1 6 Nghost: 7390.47 ave 7474 max 7302 min Histogram: 2 0 5 5 3 5 3 4 3 2 Neighs: 160113 ave 183769 max 133544 min Histogram: 1 4 4 2 4 3 4 3 3 4 Total # of neighbors = 5123615 Ave neighs/atom = 562.97275 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