#------------------------------------------------------------------------------- # 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 fix 4 fixed setforce 0.0 0.0 0.0 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) = 0.25531922 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 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.43434e-06 8436 2 103.7 9.25499e-05 2812 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.26131e-06 8436 2 103.7 0.000109987 2812 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.24574e-06 8436 2 103.7 9.31323e-05 2812 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.24357e-06 8436 2 103.7 9.23602e-05 2812 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.23452e-06 8436 2 103.7 9.66876e-05 2812 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.28008e-06 8436 2 103.7 0.000108158 2812 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.31918e-06 8436 2 103.7 0.000104344 2812 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.2584e-06 8436 2 103.7 9.05248e-05 2812 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.11117e-06 8436 2 103.7 9.19451e-05 2812 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.19702e-06 8436 2 103.7 9.11884e-05 2812 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.33361e-06 8436 2 103.7 9.73941e-05 2812 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.18789e-06 8436 2 103.7 9.64198e-05 2812 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.50324e-06 8436 2 103.7 0.000107369 2812 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.16059e-06 8436 2 103.7 9.82189e-05 2812 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.529e-06 8436 2 103.7 0.000113977 2812 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.42475e-06 8436 2 103.7 0.000103147 2812 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.03116e-06 8436 2 103.7 0.000119205 2812 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.56586e-06 8436 2 103.7 0.000132971 2812 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.34711e-06 8436 2 103.7 9.33948e-05 2812 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.61041e-06 8436 2 103.7 9.31654e-05 2812 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.07956e-06 8436 2 103.7 0.000102567 2812 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.07994e-06 8436 2 103.7 8.98787e-05 2812 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.31527e-06 8436 2 103.7 9.34222e-05 2812 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.71363e-06 8436 2 103.7 0.000101572 2812 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.35794e-06 8436 2 103.7 9.40676e-05 2812 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.20925e-06 8436 2 103.7 8.87071e-05 2812 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.45086e-06 8436 2 103.7 0.000112997 2812 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.7265e-06 8436 2 103.7 0.000136809 2812 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.10305e-06 8436 2 103.7 0.000107765 2812 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.29461e-06 8436 2 103.7 0.000111759 2812 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.3178e-06 8436 2 103.7 9.86797e-05 2812 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.41069e-06 8436 2 103.7 0.000103447 2812 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.4333e-06 8436 2 103.7 0.000100014 2812 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.42978e-06 8436 2 103.7 0.000102348 2812 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.57254e-06 8436 2 103.7 0.00011142 2812 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.12342e-06 8436 2 103.7 0.000129759 2812 2000000 2000000 396.97584 129126.99 1.4116283 298.99572 45.323916 68.663968 0 0 29528.21 -19193.124 -297.66192 -267784.35 -257335.28 6366.1949 Loop time of 30735.9 on 16 procs for 2000000 steps with 10468 atoms Performance: 5.622 ns/day, 4.269 hours/ns, 65.070 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 | 6233.3 | 17469 | 22486 |4960.7 | 56.84 Bond | 2.6478 | 8.5892 | 15.993 | 130.3 | 0.03 Kspace | 5020.9 | 10031 | 21298 |6561.5 | 32.64 Neigh | 1254 | 1255.8 | 1257.9 | 4.0 | 4.09 Comm | 707.71 | 845.86 | 908.64 | 266.9 | 2.75 Output | 0.016612 | 0.018649 | 0.02041 | 0.9 | 0.00 Modify | 1022.6 | 1066.9 | 1175 | 191.1 | 3.47 Other | | 57.92 | | | 0.19 Nlocal: 654.25 ave 781 max 367 min Histogram: 4 0 0 0 0 0 0 0 3 9 Nghost: 8627.81 ave 10055 max 7315 min Histogram: 4 0 0 4 0 4 0 0 0 4 Neighs: 323281 ave 430587 max 110070 min Histogram: 4 0 0 0 0 0 0 3 2 7 Total # of neighbors = 5172499 Ave neighs/atom = 494.12486 Ave special neighs/atom = 1.6709973 Neighbor list builds = 99352 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) = 0.25531922 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 2000000 2 0.97 1.12342e-06 8436 2 103.7 0.000129759 2812 Per MPI rank memory allocation (min/avg/max) = 13.13 | 14.25 | 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 2000000 2000000 397.67218 129126.99 1.4116283 298.99572 45.323916 68.663968 0 0 29528.21 -19193.124 -297.66192 -267784.35 -257335.28 6366.1949 Loop time of 4.47319e-06 on 16 procs for 0 steps with 10468 atoms 114.6% 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 | | 4.473e-06 | | |100.00 Nlocal: 654.25 ave 781 max 367 min Histogram: 4 0 0 0 0 0 0 0 3 9 Nghost: 8627.81 ave 10055 max 7315 min Histogram: 4 0 0 4 0 4 0 0 0 4 Neighs: 323281 ave 430587 max 110070 min Histogram: 4 0 0 0 0 0 0 3 2 7 Total # of neighbors = 5172499 Ave neighs/atom = 494.12486 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