#------------------------------------------------------------------------------- # 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 1 b 1 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 2000 = # 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) = 0.25348658 grid = 24 24 40 stencil order = 5 estimated absolute RMS force accuracy = 0.0030125684 estimated relative force accuracy = 9.0722602e-06 using double precision KISS FFT 3d grid and FFT values/proc = 4332 1152 generated 0 of 1 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 1 0.999099 0.0498115 6000 1 97.9919 9.71565 2000 Per MPI rank memory allocation (min/avg/max) = 9.965 | 9.995 | 10.03 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 -2276.0373 59830.193 1.0000033 447.33728 0 0 0 0 8647.375 64778.884 -104.25214 -104361.1 -30934.84 5332.3765 SHAKE stats (type/ave/delta/count) on step 50000 1 0.97 1.30724e-06 6000 1 103.7 9.85322e-05 2000 SHAKE stats (type/ave/delta/count) on step 100000 1 0.97 1.05953e-06 6000 1 103.7 9.30775e-05 2000 SHAKE stats (type/ave/delta/count) on step 150000 1 0.97 1.06328e-06 6000 1 103.7 8.70546e-05 2000 SHAKE stats (type/ave/delta/count) on step 200000 1 0.97 1.14136e-06 6000 1 103.7 0.000107864 2000 SHAKE stats (type/ave/delta/count) on step 250000 1 0.97 1.50262e-06 6000 1 103.7 0.000100094 2000 SHAKE stats (type/ave/delta/count) on step 300000 1 0.97 1.48126e-06 6000 1 103.7 0.000109994 2000 SHAKE stats (type/ave/delta/count) on step 350000 1 0.97 1.05478e-06 6000 1 103.7 0.000108221 2000 SHAKE stats (type/ave/delta/count) on step 400000 1 0.97 1.63779e-06 6000 1 103.7 0.000123882 2000 SHAKE stats (type/ave/delta/count) on step 450000 1 0.97 1.25404e-06 6000 1 103.7 9.59076e-05 2000 SHAKE stats (type/ave/delta/count) on step 500000 1 0.97 1.26545e-06 6000 1 103.7 9.64868e-05 2000 SHAKE stats (type/ave/delta/count) on step 550000 1 0.97 1.21686e-06 6000 1 103.7 0.000100717 2000 SHAKE stats (type/ave/delta/count) on step 600000 1 0.97 1.67012e-06 6000 1 103.7 0.000125732 2000 SHAKE stats (type/ave/delta/count) on step 650000 1 0.97 1.4733e-06 6000 1 103.7 9.47626e-05 2000 SHAKE stats (type/ave/delta/count) on step 700000 1 0.97 1.85277e-06 6000 1 103.7 0.000121162 2000 SHAKE stats (type/ave/delta/count) on step 750000 1 0.97 1.18872e-06 6000 1 103.7 9.4588e-05 2000 SHAKE stats (type/ave/delta/count) on step 800000 1 0.97 1.28382e-06 6000 1 103.7 9.09153e-05 2000 SHAKE stats (type/ave/delta/count) on step 850000 1 0.97 1.4331e-06 6000 1 103.7 0.000100882 2000 SHAKE stats (type/ave/delta/count) on step 900000 1 0.97 1.23818e-06 6000 1 103.7 0.000141697 2000 SHAKE stats (type/ave/delta/count) on step 950000 1 0.97 1.23626e-06 6000 1 103.7 8.94444e-05 2000 SHAKE stats (type/ave/delta/count) on step 1000000 1 0.97 1.10584e-06 6000 1 103.7 9.1532e-05 2000 SHAKE stats (type/ave/delta/count) on step 1050000 1 0.97 1.93111e-06 6000 1 103.7 0.000125692 2000 SHAKE stats (type/ave/delta/count) on step 1100000 1 0.97 1.35899e-06 6000 1 103.7 0.000108611 2000 SHAKE stats (type/ave/delta/count) on step 1150000 1 0.97 1.17431e-06 6000 1 103.7 9.50952e-05 2000 SHAKE stats (type/ave/delta/count) on step 1200000 1 0.97 1.58006e-06 6000 1 103.7 0.000125211 2000 SHAKE stats (type/ave/delta/count) on step 1250000 1 0.97 1.30974e-06 6000 1 103.7 9.59098e-05 2000 SHAKE stats (type/ave/delta/count) on step 1300000 1 0.97 1.53963e-06 6000 1 103.7 0.000112889 2000 SHAKE stats (type/ave/delta/count) on step 1350000 1 0.97 1.43217e-06 6000 1 103.7 0.000123861 2000 SHAKE stats (type/ave/delta/count) on step 1400000 1 0.97 1.69909e-06 6000 1 103.7 0.000119922 2000 SHAKE stats (type/ave/delta/count) on step 1450000 1 0.97 1.16762e-06 6000 1 103.7 9.89672e-05 2000 SHAKE stats (type/ave/delta/count) on step 1500000 1 0.97 1.12366e-06 6000 1 103.7 8.985e-05 2000 SHAKE stats (type/ave/delta/count) on step 1550000 1 0.97 1.21222e-06 6000 1 103.7 0.000101956 2000 SHAKE stats (type/ave/delta/count) on step 1600000 1 0.97 1.10502e-06 6000 1 103.7 9.04209e-05 2000 SHAKE stats (type/ave/delta/count) on step 1650000 1 0.97 1.38861e-06 6000 1 103.7 0.000115222 2000 SHAKE stats (type/ave/delta/count) on step 1700000 1 0.97 1.24193e-06 6000 1 103.7 9.25348e-05 2000 SHAKE stats (type/ave/delta/count) on step 1750000 1 0.97 1.09067e-06 6000 1 103.7 8.78332e-05 2000 SHAKE stats (type/ave/delta/count) on step 1800000 1 0.97 1.22724e-06 6000 1 103.7 9.67963e-05 2000 SHAKE stats (type/ave/delta/count) on step 1850000 1 0.97 2.32684e-06 6000 1 103.7 0.000184247 2000 SHAKE stats (type/ave/delta/count) on step 1900000 1 0.97 1.34418e-06 6000 1 103.7 0.00010861 2000 SHAKE stats (type/ave/delta/count) on step 1950000 1 0.97 1.2939e-06 6000 1 103.7 0.00012774 2000 SHAKE stats (type/ave/delta/count) on step 2000000 1 0.97 1.33266e-06 6000 1 103.7 0.000117288 2000 2000000 2000000 35.427789 59830.193 1.0000033 301.67629 0 0 0 0 5110.1384 77641.538 -104.25214 -104333.67 -21581.996 3596.0596 Loop time of 10316.7 on 32 procs for 2000000 steps with 6000 atoms Performance: 16.750 ns/day, 1.433 hours/ns, 193.861 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 | 5791.1 | 6059 | 6278.8 | 147.0 | 58.73 Bond | 1.9973 | 2.2116 | 3.2252 | 14.6 | 0.02 Kspace | 2104.9 | 2325.8 | 2589.5 | 235.7 | 22.54 Neigh | 328.34 | 328.85 | 329.33 | 1.7 | 3.19 Comm | 829.37 | 843.25 | 853.06 | 19.4 | 8.17 Output | 0.0078948 | 0.0099006 | 0.011706 | 1.2 | 0.00 Modify | 719.49 | 724.62 | 733.65 | 15.7 | 7.02 Other | | 32.87 | | | 0.32 Nlocal: 187.5 ave 203 max 171 min Histogram: 3 3 0 3 3 7 5 5 2 1 Nghost: 6548.84 ave 6625 max 6463 min Histogram: 3 1 2 2 7 3 7 1 3 3 Neighs: 107970 ave 115901 max 97477 min Histogram: 3 2 3 2 3 1 4 5 6 3 Total # of neighbors = 3455048 Ave neighs/atom = 575.84133 Ave special neighs/atom = 2 Neighbor list builds = 98540 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) = 0.25348658 grid = 24 24 40 stencil order = 5 estimated absolute RMS force accuracy = 0.0030125684 estimated relative force accuracy = 9.0722602e-06 using double precision KISS FFT 3d grid and FFT values/proc = 4332 1152 generated 0 of 1 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 1 0.97 1.33266e-06 6000 1 103.7 0.000117288 2000 Per MPI rank memory allocation (min/avg/max) = 9.972 | 9.997 | 10.03 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 36.215198 59830.193 1.0000033 301.67629 0 0 0 0 5110.1384 77641.538 -104.25214 -104333.67 -21581.996 3596.0596 Loop time of 7.03412e-06 on 32 procs for 0 steps with 6000 atoms 116.8% 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 | | 7.034e-06 | | |100.00 Nlocal: 187.5 ave 203 max 171 min Histogram: 3 3 0 3 3 7 5 5 2 1 Nghost: 6548.84 ave 6625 max 6463 min Histogram: 3 1 2 2 7 3 7 1 3 3 Neighs: 107970 ave 115901 max 97477 min Histogram: 3 2 3 2 3 1 4 5 6 3 Total # of neighbors = 3455048 Ave neighs/atom = 575.84133 Ave special neighs/atom = 2 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken log 2.5_NPT.out