#------------------------------------------------------------------------------- # 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 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 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) = 0.25412453 grid = 30 30 40 stencil order = 5 estimated absolute RMS force accuracy = 0.0036519507 estimated relative force accuracy = 1.0997741e-05 using double precision KISS FFT 3d grid and FFT values/proc = 5236 1800 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.997025 0.587937 8436 2 97.456 38.7086 2812 Per MPI rank memory allocation (min/avg/max) = 12.86 | 12.96 | 13.14 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 17103.337 93962.523 1.2789064 429.73544 192.00064 287.52719 0 0 22659.351 59106.549 -220.49494 -204259.25 -122013.82 8166.1181 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.52676e-06 8436 2 103.7 9.83092e-05 2812 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.26371e-06 8436 2 103.7 9.53162e-05 2812 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.42173e-06 8436 2 103.7 9.61212e-05 2812 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.60567e-06 8436 2 103.7 0.000104296 2812 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.36795e-06 8436 2 103.7 0.000113149 2812 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.07483e-06 8436 2 103.7 0.00010344 2812 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.30505e-06 8436 2 103.7 9.58147e-05 2812 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.26934e-06 8436 2 103.7 0.000111156 2812 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.33359e-06 8436 2 103.7 0.000111215 2812 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.21759e-06 8436 2 103.7 9.2651e-05 2812 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.25638e-06 8436 2 103.7 9.66165e-05 2812 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.24984e-06 8436 2 103.7 0.000104701 2812 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.11486e-06 8436 2 103.7 0.000105564 2812 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.14218e-06 8436 2 103.7 8.90542e-05 2812 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.55704e-06 8436 2 103.7 9.00981e-05 2812 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.57763e-06 8436 2 103.7 9.90362e-05 2812 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.36965e-06 8436 2 103.7 0.000133901 2812 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.2217e-06 8436 2 103.7 9.19484e-05 2812 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.12225e-06 8436 2 103.7 9.68871e-05 2812 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.22143e-06 8436 2 103.7 9.22187e-05 2812 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.3017e-06 8436 2 103.7 0.000102091 2812 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.3832e-06 8436 2 103.7 0.000111742 2812 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.19927e-06 8436 2 103.7 9.25213e-05 2812 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.38574e-06 8436 2 103.7 9.85383e-05 2812 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.2446e-06 8436 2 103.7 9.60164e-05 2812 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.27765e-06 8436 2 103.7 9.7722e-05 2812 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.48363e-06 8436 2 103.7 0.000102116 2812 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.28961e-06 8436 2 103.7 8.84282e-05 2812 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.77053e-06 8436 2 103.7 0.00012218 2812 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.68896e-06 8436 2 103.7 0.000126443 2812 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.36019e-06 8436 2 103.7 0.000102553 2812 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.48038e-06 8436 2 103.7 9.64805e-05 2812 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.37431e-06 8436 2 103.7 9.16299e-05 2812 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.15497e-06 8436 2 103.7 0.000110672 2812 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.2491e-06 8436 2 103.7 9.81224e-05 2812 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.36221e-06 8436 2 103.7 0.000105495 2812 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.47931e-06 8436 2 103.7 0.000100155 2812 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.83633e-06 8436 2 103.7 0.000120724 2812 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.78408e-06 8436 2 103.7 0.000131852 2812 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.35305e-06 8436 2 103.7 9.85387e-05 2812 2000000 2000000 1923.7953 93962.523 1.2789064 289.94673 42.448003 74.567025 0 0 19546.342 44794.454 -220.49494 -205641.51 -141183.7 5509.7603 Loop time of 14672.5 on 32 procs for 2000000 steps with 9188 atoms Performance: 11.777 ns/day, 2.038 hours/ns, 136.310 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 | 8263.9 | 8934.7 | 9509 | 287.8 | 60.89 Bond | 2.5238 | 5.4195 | 9.3798 | 84.6 | 0.04 Kspace | 2653 | 3231.8 | 3910.2 | 481.3 | 22.03 Neigh | 502.56 | 503.44 | 504.24 | 1.8 | 3.43 Comm | 965.7 | 990.36 | 1003.7 | 32.4 | 6.75 Output | 0.012853 | 0.015166 | 0.017304 | 1.1 | 0.00 Modify | 953.52 | 963.63 | 982.38 | 28.5 | 6.57 Other | | 43.14 | | | 0.29 Nlocal: 287.125 ave 313 max 275 min Histogram: 5 8 7 4 1 2 1 1 1 2 Nghost: 7332.56 ave 7403 max 7257 min Histogram: 2 3 1 5 6 4 3 3 1 4 Neighs: 161246 ave 182435 max 149998 min Histogram: 4 4 8 5 4 3 1 0 2 1 Total # of neighbors = 5159876 Ave neighs/atom = 561.58859 Ave special neighs/atom = 1.9037875 Neighbor list builds = 98793 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) = 0.25412453 grid = 30 30 40 stencil order = 5 estimated absolute RMS force accuracy = 0.0036519507 estimated relative force accuracy = 1.0997741e-05 using double precision KISS FFT 3d grid and FFT values/proc = 5236 1800 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.35305e-06 8436 2 103.7 9.85387e-05 2812 Per MPI rank memory allocation (min/avg/max) = 12.88 | 13.04 | 13.15 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 1924.6119 93962.523 1.2789064 289.94673 42.448003 74.567025 0 0 19546.342 44794.454 -220.49494 -205641.51 -141183.7 5509.7603 Loop time of 1.25713e-05 on 32 procs for 0 steps with 9188 atoms 111.9% 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 | | 1.257e-05 | | |100.00 Nlocal: 287.125 ave 313 max 275 min Histogram: 5 8 7 4 1 2 1 1 1 2 Nghost: 7332.56 ave 7403 max 7257 min Histogram: 2 3 1 5 6 4 3 3 1 4 Neighs: 161246 ave 182435 max 149998 min Histogram: 4 4 8 5 4 3 1 0 2 1 Total # of neighbors = 5159876 Ave neighs/atom = 561.58859 Ave special neighs/atom = 1.9037875 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken log 2.5_NPT.out