#------------------------------------------------------------------------------- # Stage 2.5: NPT integration for 2 ns with a timestep of 1 fs # Temperature 298.2 K # Pressure 1 atm #------------------------------------------------------------------------------- # 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 2768 = # 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 npt temp 298.2 298.2 100 iso 1 1 100 drag 0 mtk yes nreset 40000 fix 2 movable ave/time 1 199999 200000 v_time c_thermo_temp c_thermo_press v_sysvol v_sysdensity v_etotal v_cella v_cellb v_cellc v_cellalpha v_cellbeta v_cellgamma v_pe v_ke v_evdwl v_coulomb v_sxx v_syy v_szz v_syz v_sxz v_sxy file 2.5_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_cella v_cellb v_cellc v_cellalpha v_cellbeta v_cellgamma v_pe v_ke v_evdwl v_coulomb v_sxx v_syy v_szz v_syz v_sxz v_sxy file 2.5_instantaneous.txt restart 2000000 2.5.restart dump sci all custom 200000 2.5.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) = 0.32734069 grid = 45 45 45 stencil order = 5 estimated absolute RMS force accuracy = 0.0029667961 estimated relative force accuracy = 8.9344182e-06 using double precision KISS FFT 3d grid and FFT values/proc = 9396 4050 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.97 7.55507e-13 8304 2 103.7 7.79181e-11 2768 Per MPI rank memory allocation (min/avg/max) = 12.66 | 13.14 | 13.34 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 2798.553 92859.489 1.3074058 297.16539 38.366501 73.386745 0 0 22353.541 89612.049 -448.40969 -273869.34 -161792 5608.845 SHAKE stats (type/ave/delta/count) on step 50000 2 0.969949 1.47492e-06 8304 2 103.7 0.000108949 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.970009 1.43453e-06 8304 2 103.7 0.000103026 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.970012 1.15516e-06 8304 2 103.7 9.31323e-05 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.969937 1.40649e-06 8304 2 103.7 0.000112891 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.969998 1.40888e-06 8304 2 103.7 8.89915e-05 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.970015 1.22739e-06 8304 2 103.7 9.45528e-05 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.969927 1.21092e-06 8304 2 103.7 0.000111405 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.969949 1.34813e-06 8304 2 103.7 0.000112329 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.969991 1.22489e-06 8304 2 103.7 9.5234e-05 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.970064 1.76489e-06 8304 2 103.7 0.000167369 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.969961 1.26188e-06 8304 2 103.7 0.000125206 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97001 1.42615e-06 8304 2 103.7 0.000104891 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97009 1.19031e-06 8304 2 103.7 9.31052e-05 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.969954 1.27623e-06 8304 2 103.7 9.36225e-05 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.969937 1.1834e-06 8304 2 103.7 0.000101753 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.970031 1.20323e-06 8304 2 103.7 9.47432e-05 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.970051 1.39915e-06 8304 2 103.7 0.000101851 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.970136 1.62963e-06 8304 2 103.7 0.000111991 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.969992 1.70286e-06 8304 2 103.7 0.000104999 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.96999 1.11301e-06 8304 2 103.7 0.000120838 2768 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.969995 1.5568e-06 8304 2 103.7 0.000107819 2768 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.969944 1.56003e-06 8304 2 103.7 0.000115585 2768 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.970102 1.57505e-06 8304 2 103.7 0.000101908 2768 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97004 1.35816e-06 8304 2 103.7 9.11665e-05 2768 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.970076 1.52827e-06 8304 2 103.7 0.000126972 2768 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.970011 1.37075e-06 8304 2 103.7 0.000107771 2768 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.969992 1.39974e-06 8304 2 103.7 9.223e-05 2768 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.969949 1.5249e-06 8304 2 103.7 0.000102979 2768 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.970032 1.27884e-06 8304 2 103.7 0.000105203 2768 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97003 1.21792e-06 8304 2 103.7 0.000107798 2768 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.969959 1.26528e-06 8304 2 103.7 9.76425e-05 2768 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.969973 1.3257e-06 8304 2 103.7 0.000111363 2768 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.96996 1.45529e-06 8304 2 103.7 0.000131962 2768 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.970032 1.1589e-06 8304 2 103.7 9.65442e-05 2768 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.96996 1.21675e-06 8304 2 103.7 0.000100873 2768 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.969993 1.3225e-06 8304 2 103.7 9.07757e-05 2768 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.969997 2.1411e-06 8304 2 103.7 0.000110404 2768 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.970009 1.34757e-06 8304 2 103.7 0.000102127 2768 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.970017 1.63583e-06 8304 2 103.7 0.000113031 2768 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97001 1.38507e-06 8304 2 103.7 0.000100332 2768 2000000 2000000 433.30756 96967.088 1.2520231 297.30924 35.499493 60.418217 0 0 21423.07 90872.206 -429.41472 -273853.44 -161462.24 5611.5601 Loop time of 12380.1 on 32 procs for 2000000 steps with 9101 atoms Performance: 13.958 ns/day, 1.719 hours/ns, 161.550 timesteps/s 99.2% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4287.9 | 4466.3 | 4719.5 | 156.8 | 36.08 Bond | 2.4031 | 5.5139 | 10.783 | 109.8 | 0.04 Kspace | 4362.5 | 4609.1 | 4787.3 | 154.0 | 37.23 Neigh | 324.72 | 325.9 | 327.07 | 5.0 | 2.63 Comm | 718.38 | 735.42 | 753.36 | 29.1 | 5.94 Output | 0.0086293 | 0.010829 | 0.012906 | 1.3 | 0.00 Modify | 1469.1 | 1797.6 | 2152.9 | 658.6 | 14.52 Other | | 440.2 | | | 3.56 Nlocal: 284.406 ave 306 max 265 min Histogram: 2 2 3 5 8 5 3 1 0 3 Nghost: 4847.66 ave 4908 max 4788 min Histogram: 3 1 0 7 5 8 1 1 3 3 Neighs: 84889.2 ave 96133 max 78161 min Histogram: 2 2 7 11 4 2 2 0 0 2 Total # of neighbors = 2716456 Ave neighs/atom = 298.47885 Ave special neighs/atom = 1.8929788 Neighbor list builds = 102629 Dangerous builds = 0 undump sci restart 0 dump sci all custom 2000000 2.5.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) = 0.32625292 grid = 45 45 45 stencil order = 5 estimated absolute RMS force accuracy = 0.0030966694 estimated relative force accuracy = 9.3255278e-06 using double precision KISS FFT 3d grid and FFT values/proc = 9396 4050 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97001 1.38507e-06 8304 2 103.7 0.000100332 2768 Per MPI rank memory allocation (min/avg/max) = 12.67 | 13.18 | 13.35 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 491.52545 96967.088 1.2520231 297.30924 35.499493 60.418217 0 0 21423.07 89980.848 -429.41472 -272962.08 -161462.24 5611.5601 Loop time of 7.26869e-06 on 32 procs for 0 steps with 9101 atoms 123.0% 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 | | 7.269e-06 | | |100.00 Nlocal: 284.406 ave 306 max 265 min Histogram: 2 2 3 5 8 5 3 1 0 3 Nghost: 4847.66 ave 4908 max 4788 min Histogram: 3 1 0 7 5 8 1 1 3 3 Neighs: 84889.2 ave 96133 max 78161 min Histogram: 2 2 7 11 4 2 2 0 0 2 Total # of neighbors = 2716456 Ave neighs/atom = 298.47885 Ave special neighs/atom = 1.8929788 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken Total wall time: 6:35:44