#------------------------------------------------------------------------------- # Stage 2.4: NVT integration for 1 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 2812 = # 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 100000 100000 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 100 1 100 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 fix 4 fixed setforce 0.0 0.0 0.0 restart 1000000 2.4.restart dump sci all custom 100000 2.4.xyz id mol type q xs ys zs timestep 1 run 1000000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.25537807 grid = 30 30 64 stencil order = 5 estimated absolute RMS force accuracy = 0.0034433421 estimated relative force accuracy = 1.0369522e-05 using double precision KISS FFT 3d grid and FFT values/proc = 11132 3600 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 1.0002 0.0681427 8436 2 97.8082 10.2822 2812 Per MPI rank memory allocation (min/avg/max) = 12.83 | 14.13 | 14.79 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 -2464.2585 141184.09 1.4079299 407.8254 6.8700056 32.065233 0 0 34600.933 -53340.346 -312.04795 -284230.57 -302931.04 9325.2516 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.14835e-06 8436 2 103.7 9.11627e-05 2812 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.21747e-06 8436 2 103.7 0.000101938 2812 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.34512e-06 8436 2 103.7 0.000119952 2812 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.40216e-06 8436 2 103.7 0.000109449 2812 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.12245e-06 8436 2 103.7 9.22926e-05 2812 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.46115e-06 8436 2 103.7 9.34053e-05 2812 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.33971e-06 8436 2 103.7 0.000101063 2812 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.22989e-06 8436 2 103.7 9.88347e-05 2812 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.22573e-06 8436 2 103.7 0.000127887 2812 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.66532e-06 8436 2 103.7 9.2873e-05 2812 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.22373e-06 8436 2 103.7 9.53794e-05 2812 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.07954e-06 8436 2 103.7 9.35481e-05 2812 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.48629e-06 8436 2 103.7 0.00010539 2812 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.04915e-06 8436 2 103.7 9.83138e-05 2812 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.44837e-06 8436 2 103.7 9.83663e-05 2812 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.37593e-06 8436 2 103.7 9.06875e-05 2812 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.1916e-06 8436 2 103.7 9.86071e-05 2812 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.04937e-06 8436 2 103.7 0.000100218 2812 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.27441e-06 8436 2 103.7 8.84432e-05 2812 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.17428e-06 8436 2 103.7 0.000115474 2812 1000000 1000000 -288.87047 141184.09 1.4079299 296.82941 48.771212 66.923035 0 0 31887.79 -35591.428 -312.04795 -284074.92 -287662.86 6787.2401 Loop time of 13630.5 on 16 procs for 1000000 steps with 10808 atoms Performance: 6.339 ns/day, 3.786 hours/ns, 73.365 timesteps/s 98.9% CPU use with 16 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2051.3 | 7496.3 | 10492 |3599.0 | 55.00 Bond | 1.1099 | 3.3438 | 6.9792 | 89.0 | 0.02 Kspace | 1920.3 | 4925.4 | 10378 |4446.8 | 36.13 Neigh | 543.49 | 544.67 | 546.04 | 3.5 | 4.00 Comm | 233.74 | 276.65 | 299.91 | 149.9 | 2.03 Output | 0.015837 | 0.01775 | 0.019444 | 0.8 | 0.00 Modify | 346.56 | 363.43 | 399.82 | 110.4 | 2.67 Other | | 20.66 | | | 0.15 Nlocal: 675.5 ave 811 max 347 min Histogram: 4 0 0 0 0 0 0 0 2 10 Nghost: 8243.44 ave 9819 max 7129 min Histogram: 4 0 3 4 1 0 0 0 0 4 Neighs: 316377 ave 418460 max 88071 min Histogram: 4 0 0 0 0 0 0 0 4 8 Total # of neighbors = 5062025 Ave neighs/atom = 468.35909 Ave special neighs/atom = 1.6184308 Neighbor list builds = 49754 Dangerous builds = 0 undump sci restart 0 dump sci all custom 1000000 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) = 0.25537807 grid = 30 30 64 stencil order = 5 estimated absolute RMS force accuracy = 0.0034433421 estimated relative force accuracy = 1.0369522e-05 using double precision KISS FFT 3d grid and FFT values/proc = 11132 3600 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.17428e-06 8436 2 103.7 0.000115474 2812 Per MPI rank memory allocation (min/avg/max) = 12.83 | 14.23 | 14.79 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 1000000 1000000 -288.28961 141184.09 1.4079299 296.82941 48.771212 66.923035 0 0 31887.79 -35591.428 -312.04795 -284074.92 -287662.86 6787.2401 Loop time of 4.07669e-06 on 16 procs for 0 steps with 10808 atoms 136.4% CPU use with 16 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 | | 4.077e-06 | | |100.00 Nlocal: 675.5 ave 811 max 347 min Histogram: 4 0 0 0 0 0 0 0 2 10 Nghost: 8243.44 ave 9819 max 7129 min Histogram: 4 0 3 4 1 0 0 0 0 4 Neighs: 316377 ave 418460 max 88071 min Histogram: 4 0 0 0 0 0 0 0 4 8 Total # of neighbors = 5062025 Ave neighs/atom = 468.35909 Ave special neighs/atom = 1.6184308 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix 4 unfix shaken log 2.5_NVT.out