#------------------------------------------------------------------------------- # Stage 2.4: NVT integration for 10 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 1000 1000 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 1 1 1 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 10000 2.4.restart dump sci all custom 1000 2.4.xyz id mol type q xs ys zs timestep 1 run 10000 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 = 7260 1800 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 1.00022 0.0683891 8436 2 97.8065 10.268 2812 Per MPI rank memory allocation (min/avg/max) = 12.46 | 13.16 | 13.65 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 -2348.6164 141184.09 1.4079299 407.8254 6.8547611 32.216806 0 0 34634.878 -53383.538 -312.04795 -284230.21 -302939.8 9325.2516 10000 10000 -79.595375 141184.09 1.4079299 294.32343 41.895329 79.032406 0 0 32157.224 -35746.778 -312.04795 -284049.43 -287518.05 6729.939 Loop time of 97.799 on 32 procs for 10000 steps with 10808 atoms Performance: 8.834 ns/day, 2.717 hours/ns, 102.251 timesteps/s 98.9% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 12.452 | 45.188 | 66.074 | 285.3 | 46.21 Bond | 0.010249 | 0.027319 | 0.064011 | 9.6 | 0.03 Kspace | 16.191 | 37.184 | 70.115 | 315.9 | 38.02 Neigh | 4.3024 | 4.3099 | 4.3225 | 0.3 | 4.41 Comm | 3.5342 | 4.6722 | 5.1284 | 23.5 | 4.78 Output | 0.012289 | 0.014688 | 0.016989 | 1.2 | 0.02 Modify | 5.6271 | 5.9994 | 6.9125 | 17.5 | 6.13 Other | | 0.4038 | | | 0.41 Nlocal: 337.75 ave 428 max 160 min Histogram: 5 3 0 0 0 0 1 6 7 10 Nghost: 6430.44 ave 7767 max 4718 min Histogram: 8 0 0 4 4 0 0 0 6 10 Neighs: 158766 ave 231878 max 41567 min Histogram: 8 0 0 0 1 2 1 4 8 8 Total # of neighbors = 5080524 Ave neighs/atom = 470.07069 Ave special neighs/atom = 1.6184308 Neighbor list builds = 484 Dangerous builds = 0 undump sci restart 0 dump sci all custom 10000 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 = 7260 1800 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 10000 2 0.97 1.51466e-06 8436 2 103.7 0.000111105 2812 Per MPI rank memory allocation (min/avg/max) = 12.46 | 13.2 | 13.65 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 10000 10000 -79.127696 141184.09 1.4079299 294.32343 41.895329 79.032406 0 0 32157.224 -35746.778 -312.04795 -284049.43 -287518.05 6729.939 Loop time of 7.78225e-06 on 32 procs for 0 steps with 10808 atoms 116.9% 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 | | 7.782e-06 | | |100.00 Nlocal: 337.75 ave 428 max 160 min Histogram: 5 3 0 0 0 0 1 6 7 10 Nghost: 6430.44 ave 7767 max 4718 min Histogram: 8 0 0 4 4 0 0 0 6 10 Neighs: 158766 ave 231878 max 41567 min Histogram: 8 0 0 0 1 2 1 4 8 8 Total # of neighbors = 5080524 Ave neighs/atom = 470.07069 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