#------------------------------------------------------------------------------- # 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 = 0.002 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) = 0.25584802 grid = 30 30 30 stencil order = 5 estimated absolute RMS force accuracy = 0.0034810988 estimated relative force accuracy = 1.0483226e-05 using double precision KISS FFT 3d grid and FFT values/proc = 4312 960 generated 0 of 28 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.998072 0.671855 5784 2 97.1926 29.6866 1928 Per MPI rank memory allocation (min/avg/max) = 12.66 | 12.77 | 12.87 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 12638.255 65360.011 1.3291045 427.16581 39.039756 133.12616 0 0 19123.193 16123.648 -161.84744 -155223.89 -119804.88 5676.3721 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.23972e-06 5784 2 103.7 9.77235e-05 1928 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.11884e-06 5784 2 103.7 8.90199e-05 1928 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.27571e-06 5784 2 103.7 8.98322e-05 1928 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.14066e-06 5784 2 103.7 9.78326e-05 1928 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.16551e-06 5784 2 103.7 9.7009e-05 1928 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.0687e-06 5784 2 103.7 0.000106331 1928 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.27892e-06 5784 2 103.7 0.000101211 1928 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.17041e-06 5784 2 103.7 9.60384e-05 1928 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.35774e-06 5784 2 103.7 9.37468e-05 1928 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.28298e-06 5784 2 103.7 9.57944e-05 1928 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.08465e-06 5784 2 103.7 8.83427e-05 1928 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.256e-06 5784 2 103.7 0.000108828 1928 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.15833e-06 5784 2 103.7 0.000103359 1928 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.22744e-06 5784 2 103.7 8.93012e-05 1928 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.17116e-06 5784 2 103.7 9.96264e-05 1928 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.16587e-06 5784 2 103.7 9.62245e-05 1928 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.23501e-06 5784 2 103.7 9.336e-05 1928 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.01616e-06 5784 2 103.7 9.44013e-05 1928 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.32769e-06 5784 2 103.7 0.000110065 1928 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.39711e-06 5784 2 103.7 0.000108565 1928 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.20968e-06 5784 2 103.7 0.000105679 1928 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.31407e-06 5784 2 103.7 0.000102874 1928 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.63571e-06 5784 2 103.7 0.000111339 1928 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.33647e-06 5784 2 103.7 9.87735e-05 1928 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.10537e-06 5784 2 103.7 8.86414e-05 1928 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.13922e-06 5784 2 103.7 0.000109139 1928 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.14678e-06 5784 2 103.7 0.000104565 1928 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.14113e-06 5784 2 103.7 0.000103318 1928 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.27219e-06 5784 2 103.7 0.000100639 1928 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.15002e-06 5784 2 103.7 9.13929e-05 1928 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.4767e-06 5784 2 103.7 0.000112712 1928 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.35197e-06 5784 2 103.7 0.000112531 1928 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.3005e-06 5784 2 103.7 0.000103114 1928 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.22001e-06 5784 2 103.7 9.15147e-05 1928 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.40948e-06 5784 2 103.7 0.000141732 1928 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.1734e-06 5784 2 103.7 9.25312e-05 1928 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.27491e-06 5784 2 103.7 9.81568e-05 1928 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.80637e-06 5784 2 103.7 0.000123144 1928 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.35367e-06 5784 2 103.7 0.000129764 1928 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.26664e-06 5784 2 103.7 8.95903e-05 1928 2000000 2000000 2810.9718 65360.011 1.3291045 300.78708 32.049327 39.581224 0 0 17143.89 12588.21 -161.84744 -155734.68 -125930.95 3996.9944 Loop time of 10984.1 on 32 procs for 2000000 steps with 6387 atoms Performance: 15.732 ns/day, 1.526 hours/ns, 182.081 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 | 5648.8 | 6402.8 | 7142.4 | 536.8 | 58.29 Bond | 2.0333 | 4.1563 | 7.9509 | 90.3 | 0.04 Kspace | 1853.9 | 2601.4 | 3357.1 | 843.4 | 23.68 Neigh | 368.47 | 368.85 | 369.25 | 1.1 | 3.36 Comm | 841.47 | 851.62 | 862.66 | 18.8 | 7.75 Output | 0.0082509 | 0.010165 | 0.011965 | 1.1 | 0.00 Modify | 715.4 | 721.03 | 727.72 | 11.1 | 6.56 Other | | 34.26 | | | 0.31 Nlocal: 199.594 ave 219 max 175 min Histogram: 2 1 0 3 6 5 7 5 1 2 Nghost: 6636.22 ave 6691 max 6592 min Histogram: 4 3 6 3 2 3 2 6 1 2 Neighs: 112014 ave 126473 max 92930 min Histogram: 1 1 3 3 7 3 4 3 2 5 Total # of neighbors = 3584447 Ave neighs/atom = 561.2098 Ave special neighs/atom = 1.8738062 Neighbor list builds = 94974 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) = 0.25584802 grid = 30 30 30 stencil order = 5 estimated absolute RMS force accuracy = 0.0034810988 estimated relative force accuracy = 1.0483226e-05 using double precision KISS FFT 3d grid and FFT values/proc = 4312 960 generated 0 of 28 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.26664e-06 5784 2 103.7 8.95903e-05 1928 Per MPI rank memory allocation (min/avg/max) = 12.66 | 12.8 | 12.87 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 2811.8874 65360.011 1.3291045 300.78708 32.049327 39.581224 0 0 17143.89 12588.21 -161.84744 -155734.68 -125930.95 3996.9944 Loop time of 7.242e-06 on 32 procs for 0 steps with 6387 atoms 113.5% 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 | | 7.242e-06 | | |100.00 Nlocal: 199.594 ave 219 max 175 min Histogram: 2 1 0 3 6 5 7 5 1 2 Nghost: 6636.22 ave 6691 max 6592 min Histogram: 4 3 6 3 2 3 2 6 1 2 Neighs: 112014 ave 126473 max 92930 min Histogram: 1 1 3 3 7 3 4 3 2 5 Total # of neighbors = 3584447 Ave neighs/atom = 561.2098 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