#------------------------------------------------------------------------------- # 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 1928 = # 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) = 0.32729257 grid = 40 40 40 stencil order = 5 estimated absolute RMS force accuracy = 0.0030709373 estimated relative force accuracy = 9.2480364e-06 using double precision KISS FFT 3d grid and FFT values/proc = 7803 3200 generated 0 of 28 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.997088 0.670067 5784 2 97.1098 20.3208 1928 Per MPI rank memory allocation (min/avg/max) = 12.42 | 12.55 | 12.72 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 12695.435 65360.011 1.3291045 427.16581 36.267606 124.56562 0 0 18665.935 57903.198 -321.48015 -197696.72 -120966.76 5676.3721 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.16348e-06 5784 2 103.7 0.000106815 1928 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.23423e-06 5784 2 103.7 9.39971e-05 1928 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.15207e-06 5784 2 103.7 0.000107259 1928 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.16961e-06 5784 2 103.7 0.0001146 1928 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.49726e-06 5784 2 103.7 0.000111533 1928 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.27316e-06 5784 2 103.7 9.27401e-05 1928 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.35807e-06 5784 2 103.7 0.000135498 1928 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.33868e-06 5784 2 103.7 0.000106616 1928 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.0233e-06 5784 2 103.7 8.44012e-05 1928 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.02558e-06 5784 2 103.7 9.23759e-05 1928 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 2.33607e-06 5784 2 103.7 0.000159308 1928 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.10684e-06 5784 2 103.7 9.1898e-05 1928 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.40783e-06 5784 2 103.7 9.66543e-05 1928 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.25385e-06 5784 2 103.7 0.000104979 1928 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.53195e-06 5784 2 103.7 0.000116569 1928 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.25954e-06 5784 2 103.7 0.00010712 1928 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.52702e-06 5784 2 103.7 0.000116927 1928 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.66611e-06 5784 2 103.7 0.000112415 1928 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.56506e-06 5784 2 103.7 0.000128091 1928 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.41915e-06 5784 2 103.7 9.69409e-05 1928 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.13192e-06 5784 2 103.7 8.99815e-05 1928 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.54916e-06 5784 2 103.7 0.000102319 1928 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.29391e-06 5784 2 103.7 9.35684e-05 1928 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.20678e-06 5784 2 103.7 9.59118e-05 1928 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.25841e-06 5784 2 103.7 9.44198e-05 1928 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.49894e-06 5784 2 103.7 0.000107335 1928 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.31715e-06 5784 2 103.7 0.000103636 1928 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.06016e-06 5784 2 103.7 0.000111398 1928 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.34093e-06 5784 2 103.7 9.77497e-05 1928 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.28104e-06 5784 2 103.7 0.000107302 1928 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.27999e-06 5784 2 103.7 0.000126488 1928 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.29274e-06 5784 2 103.7 0.00010188 1928 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.25568e-06 5784 2 103.7 9.1859e-05 1928 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.24422e-06 5784 2 103.7 9.00939e-05 1928 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.48227e-06 5784 2 103.7 0.000105882 1928 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.33651e-06 5784 2 103.7 0.000115495 1928 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.11125e-06 5784 2 103.7 0.000100122 1928 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.45187e-06 5784 2 103.7 9.45038e-05 1928 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.23385e-06 5784 2 103.7 9.43522e-05 1928 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.22952e-06 5784 2 103.7 0.000100267 1928 2000000 2000000 2800.7327 65360.011 1.3291045 293.55129 37.686133 49.021544 0 0 17152.633 55390.954 -321.48015 -198518.76 -125888.46 3900.842 Loop time of 8188.45 on 32 procs for 2000000 steps with 6387 atoms Performance: 21.103 ns/day, 1.137 hours/ns, 244.246 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 | 3058.1 | 3404.8 | 3733.4 | 324.7 | 41.58 Bond | 1.6614 | 4.0411 | 7.0937 | 85.0 | 0.05 Kspace | 3046.3 | 3375.6 | 3723.3 | 326.2 | 41.22 Neigh | 195.96 | 196.79 | 197.45 | 3.6 | 2.40 Comm | 578.92 | 590.24 | 597.67 | 18.6 | 7.21 Output | 0.0096325 | 0.011603 | 0.013402 | 1.1 | 0.00 Modify | 583.48 | 589.87 | 599.69 | 17.3 | 7.20 Other | | 27.09 | | | 0.33 Nlocal: 199.594 ave 212 max 186 min Histogram: 3 1 1 6 6 1 4 6 1 3 Nghost: 4398.47 ave 4452 max 4340 min Histogram: 1 1 5 4 6 2 4 4 2 3 Neighs: 62011.8 ave 69507 max 54193 min Histogram: 2 2 3 5 5 3 3 3 4 2 Total # of neighbors = 1984376 Ave neighs/atom = 310.68984 Ave special neighs/atom = 1.8738062 Neighbor list builds = 95034 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) = 0.32729257 grid = 40 40 40 stencil order = 5 estimated absolute RMS force accuracy = 0.0030709373 estimated relative force accuracy = 9.2480364e-06 using double precision KISS FFT 3d grid and FFT values/proc = 7803 3200 generated 0 of 28 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.22952e-06 5784 2 103.7 0.000100267 1928 Per MPI rank memory allocation (min/avg/max) = 12.42 | 12.61 | 12.72 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 2801.6963 65360.011 1.3291045 293.55129 37.686133 49.021544 0 0 17152.633 55390.954 -321.48015 -198518.76 -125888.46 3900.842 Loop time of 8.29453e-06 on 32 procs for 0 steps with 6387 atoms 112.3% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 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 | | 8.295e-06 | | |100.00 Nlocal: 199.594 ave 212 max 186 min Histogram: 3 1 1 6 6 1 4 6 1 3 Nghost: 4398.47 ave 4452 max 4340 min Histogram: 1 1 5 4 6 2 4 4 2 3 Neighs: 62011.8 ave 69507 max 54193 min Histogram: 2 2 3 5 5 3 3 3 4 2 Total # of neighbors = 1984376 Ave neighs/atom = 310.68984 Ave special neighs/atom = 1.8738062 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken log 2.5_NPT.out