#------------------------------------------------------------------------------- # 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) = 0.25584802 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 0.995346 0.689681 5784 2 96.9616 25.3054 1928 Per MPI rank memory allocation (min/avg/max) = 12.67 | 12.76 | 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 9875.8766 65360.011 1.3291045 427.16581 30.535025 170.99747 0 0 18326.26 18593.802 -161.84744 -155278.42 -118156.83 5676.3721 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.35259e-06 5784 2 103.7 0.000109503 1928 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.57685e-06 5784 2 103.7 0.000112455 1928 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.03934e-06 5784 2 103.7 9.05968e-05 1928 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.4019e-06 5784 2 103.7 9.08876e-05 1928 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.30437e-06 5784 2 103.7 0.000122131 1928 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 2.39594e-06 5784 2 103.7 0.000161097 1928 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.19811e-06 5784 2 103.7 0.000100363 1928 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.21302e-06 5784 2 103.7 8.81547e-05 1928 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.29937e-06 5784 2 103.7 0.000123027 1928 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.36426e-06 5784 2 103.7 9.40473e-05 1928 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.2307e-06 5784 2 103.7 9.79038e-05 1928 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.18649e-06 5784 2 103.7 0.000114788 1928 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.46905e-06 5784 2 103.7 0.00012199 1928 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.23387e-06 5784 2 103.7 9.07242e-05 1928 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.31998e-06 5784 2 103.7 9.6772e-05 1928 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.30703e-06 5784 2 103.7 9.76026e-05 1928 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.28945e-06 5784 2 103.7 0.000105623 1928 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.2536e-06 5784 2 103.7 0.000122377 1928 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.27467e-06 5784 2 103.7 9.53799e-05 1928 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.28979e-06 5784 2 103.7 9.46585e-05 1928 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.48172e-06 5784 2 103.7 0.000118171 1928 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.29225e-06 5784 2 103.7 9.43576e-05 1928 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.18474e-06 5784 2 103.7 0.000101143 1928 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.32897e-06 5784 2 103.7 0.000105673 1928 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.17523e-06 5784 2 103.7 0.000102943 1928 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.05239e-06 5784 2 103.7 8.67523e-05 1928 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.10835e-06 5784 2 103.7 9.29982e-05 1928 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.26402e-06 5784 2 103.7 9.86989e-05 1928 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.50803e-06 5784 2 103.7 0.000118424 1928 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.18098e-06 5784 2 103.7 9.73075e-05 1928 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.19918e-06 5784 2 103.7 9.29101e-05 1928 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.33922e-06 5784 2 103.7 9.16712e-05 1928 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.21656e-06 5784 2 103.7 0.000110048 1928 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.17309e-06 5784 2 103.7 8.85345e-05 1928 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.27302e-06 5784 2 103.7 9.49939e-05 1928 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.44346e-06 5784 2 103.7 9.19801e-05 1928 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.56834e-06 5784 2 103.7 0.000115781 1928 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.10713e-06 5784 2 103.7 9.37655e-05 1928 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.19415e-06 5784 2 103.7 9.20492e-05 1928 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.52324e-06 5784 2 103.7 0.000119262 1928 2000000 2000000 3286.9862 65360.011 1.3291045 293.94286 25.78052 45.73139 0 0 17366.433 12334.119 -161.84744 -155728.81 -125956.75 3906.0454 Loop time of 10931.9 on 32 procs for 2000000 steps with 6387 atoms Performance: 15.807 ns/day, 1.518 hours/ns, 182.950 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 | 5794.4 | 6409.6 | 7144.8 | 410.1 | 58.63 Bond | 2.0296 | 4.261 | 8.2556 | 85.1 | 0.04 Kspace | 1813.6 | 2549.6 | 3165.4 | 651.4 | 23.32 Neigh | 365.57 | 365.93 | 366.41 | 1.3 | 3.35 Comm | 831.61 | 849.16 | 867.67 | 29.6 | 7.77 Output | 0.011457 | 0.013338 | 0.01511 | 1.0 | 0.00 Modify | 708.26 | 718.8 | 731.5 | 21.2 | 6.58 Other | | 34.54 | | | 0.32 Nlocal: 199.594 ave 217 max 187 min Histogram: 1 4 6 6 5 1 4 3 1 1 Nghost: 6630.16 ave 6653 max 6591 min Histogram: 1 0 1 3 5 2 8 2 7 3 Neighs: 112020 ave 127775 max 100494 min Histogram: 2 6 6 2 4 4 3 2 2 1 Total # of neighbors = 3584641 Ave neighs/atom = 561.24018 Ave special neighs/atom = 1.8738062 Neighbor list builds = 94846 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 1.52324e-06 5784 2 103.7 0.000119262 1928 Per MPI rank memory allocation (min/avg/max) = 12.67 | 12.85 | 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 3287.8127 65360.011 1.3291045 293.94286 25.78052 45.73139 0 0 17366.433 12334.119 -161.84744 -155728.81 -125956.75 3906.0454 Loop time of 7.93716e-06 on 32 procs for 0 steps with 6387 atoms 118.5% 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 | | 7.937e-06 | | |100.00 Nlocal: 199.594 ave 217 max 187 min Histogram: 1 4 6 6 5 1 4 3 1 1 Nghost: 6630.16 ave 6653 max 6591 min Histogram: 1 0 1 3 5 2 8 2 7 3 Neighs: 112020 ave 127775 max 100494 min Histogram: 2 6 6 2 4 4 3 2 2 1 Total # of neighbors = 3584641 Ave neighs/atom = 561.24018 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