#------------------------------------------------------------------------------- # Stage 2.4: NVT integration for 200 ps 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 20000 20000 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 20 1 20 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 200000 2.4.restart dump sci all custom 20000 2.4.xyz id mol type q xs ys zs timestep 1 run 200000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.25531922 grid = 27 27 72 stencil order = 5 estimated absolute RMS force accuracy = 0.0034643513 estimated relative force accuracy = 1.0432791e-05 using double precision KISS FFT 3d grid and FFT values/proc = 10000 3645 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.99405 0.770718 8436 2 96.1563 38.3645 2812 Per MPI rank memory allocation (min/avg/max) = 12.75 | 14.01 | 14.72 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 13788.786 129126.99 1.4116283 415.64004 144.96752 287.48191 0 0 34103.016 -3734.7595 -297.66192 -262600.99 -231800.29 8849.777 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.14405e-06 8436 2 103.7 9.34592e-05 2812 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.22288e-06 8436 2 103.7 0.000114437 2812 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.22723e-06 8436 2 103.7 9.12205e-05 2812 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.0919e-06 8436 2 103.7 9.01026e-05 2812 200000 200000 944.50274 129126.99 1.4116283 297.75324 39.120193 76.638149 0 0 29832.547 -19506.642 -297.66192 -267778.09 -257336.42 6339.74 Loop time of 3052.49 on 16 procs for 200000 steps with 10468 atoms Performance: 5.661 ns/day, 4.240 hours/ns, 65.520 timesteps/s 99.1% CPU use with 16 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 622.34 | 1749 | 2262.2 |1575.1 | 57.30 Bond | 0.25779 | 0.90293 | 1.4429 | 42.0 | 0.03 Kspace | 467.46 | 979.71 | 2110 |2109.2 | 32.10 Neigh | 124.94 | 125.19 | 125.45 | 1.4 | 4.10 Comm | 70.25 | 84.884 | 91.794 | 87.9 | 2.78 Output | 0.017063 | 0.019121 | 0.020945 | 0.9 | 0.00 Modify | 102.52 | 106.93 | 118.8 | 65.2 | 3.50 Other | | 5.86 | | | 0.19 Nlocal: 654.25 ave 765 max 368 min Histogram: 4 0 0 0 0 0 0 0 1 11 Nghost: 8645.88 ave 10121 max 7296 min Histogram: 4 0 0 4 0 4 0 0 0 4 Neighs: 323132 ave 419119 max 111453 min Histogram: 4 0 0 0 0 0 0 2 2 8 Total # of neighbors = 5170111 Ave neighs/atom = 493.89673 Ave special neighs/atom = 1.6709973 Neighbor list builds = 9988 Dangerous builds = 0 undump sci restart 0 dump sci all custom 200000 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) = 0.25531922 grid = 27 27 72 stencil order = 5 estimated absolute RMS force accuracy = 0.0034643513 estimated relative force accuracy = 1.0432791e-05 using double precision KISS FFT 3d grid and FFT values/proc = 10000 3645 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.0919e-06 8436 2 103.7 9.01026e-05 2812 Per MPI rank memory allocation (min/avg/max) = 13.13 | 14.21 | 14.72 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 200000 200000 945.15236 129126.99 1.4116283 297.75324 39.120193 76.638149 0 0 29832.547 -19506.642 -297.66192 -267778.09 -257336.42 6339.74 Loop time of 4.06906e-06 on 16 procs for 0 steps with 10468 atoms 122.9% CPU use with 16 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 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 | | 4.069e-06 | | |100.00 Nlocal: 654.25 ave 765 max 368 min Histogram: 4 0 0 0 0 0 0 0 1 11 Nghost: 8645.88 ave 10121 max 7296 min Histogram: 4 0 0 4 0 4 0 0 0 4 Neighs: 323132 ave 419119 max 111453 min Histogram: 4 0 0 0 0 0 0 2 2 8 Total # of neighbors = 5170111 Ave neighs/atom = 493.89673 Ave special neighs/atom = 1.6709973 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix 4 unfix shaken log 2.5_NVT.out