#------------------------------------------------------------------------------- # 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 1.18683e-12 8304 2 103.7 8.6942e-11 2768 Per MPI rank memory allocation (min/avg/max) = 12.82 | 13.15 | 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 2544.5752 92859.489 1.3074058 304.48972 41.735473 73.097743 0 0 22365.186 89719.609 -448.40969 -273850.55 -161650.92 5747.088 SHAKE stats (type/ave/delta/count) on step 50000 2 0.969911 1.41182e-06 8304 2 103.7 0.000117755 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.970023 1.06398e-06 8304 2 103.7 0.000102159 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.970032 1.8269e-06 8304 2 103.7 0.000124888 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.969947 1.38061e-06 8304 2 103.7 0.000111739 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.970081 1.79007e-06 8304 2 103.7 0.000125438 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.969939 1.40955e-06 8304 2 103.7 0.000114931 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.970075 1.19765e-06 8304 2 103.7 0.000107636 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.970019 1.57376e-06 8304 2 103.7 0.000115563 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.969923 1.33183e-06 8304 2 103.7 0.000128001 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.969978 1.44109e-06 8304 2 103.7 0.000117138 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.969951 1.24666e-06 8304 2 103.7 0.000107063 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.969978 1.27261e-06 8304 2 103.7 0.000107895 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.969984 1.19619e-06 8304 2 103.7 0.000112013 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.970011 1.22465e-06 8304 2 103.7 9.20068e-05 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.969995 1.59684e-06 8304 2 103.7 0.000108122 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.970004 1.19926e-06 8304 2 103.7 9.52883e-05 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.970056 1.39425e-06 8304 2 103.7 0.000108903 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.969963 1.01238e-06 8304 2 103.7 8.70744e-05 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.970092 1.54764e-06 8304 2 103.7 0.00010907 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.969999 1.04726e-06 8304 2 103.7 9.04304e-05 2768 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.969957 1.37595e-06 8304 2 103.7 0.000130168 2768 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.970092 1.60357e-06 8304 2 103.7 0.000116294 2768 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.969993 1.22478e-06 8304 2 103.7 9.70933e-05 2768 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.969971 1.1506e-06 8304 2 103.7 9.50564e-05 2768 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.970008 1.16159e-06 8304 2 103.7 9.49765e-05 2768 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.969941 1.32878e-06 8304 2 103.7 9.87335e-05 2768 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.970041 1.55881e-06 8304 2 103.7 0.000112668 2768 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.970015 1.36478e-06 8304 2 103.7 9.12838e-05 2768 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.969924 1.1415e-06 8304 2 103.7 0.000100467 2768 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.969984 1.19821e-06 8304 2 103.7 9.95346e-05 2768 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.970002 1.26676e-06 8304 2 103.7 9.63084e-05 2768 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.970019 1.42761e-06 8304 2 103.7 0.000117279 2768 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.970074 1.77383e-06 8304 2 103.7 0.00012025 2768 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.970048 1.40737e-06 8304 2 103.7 0.000102837 2768 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.969897 1.27039e-06 8304 2 103.7 0.00010475 2768 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.970013 1.53423e-06 8304 2 103.7 8.99698e-05 2768 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.970043 1.35807e-06 8304 2 103.7 9.5564e-05 2768 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.970027 2.021e-06 8304 2 103.7 0.000139499 2768 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.969982 1.32081e-06 8304 2 103.7 9.63135e-05 2768 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.969977 1.0894e-06 8304 2 103.7 8.95677e-05 2768 2000000 2000000 411.6107 97472.51 1.245531 291.97385 44.333427 82.808542 0 0 21466.082 90914.158 -427.18808 -273811.37 -161303.98 5510.8572 Loop time of 12395.6 on 32 procs for 2000000 steps with 9101 atoms Performance: 13.940 ns/day, 1.722 hours/ns, 161.348 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 | 4260.6 | 4459.3 | 4871 | 181.3 | 35.97 Bond | 2.2248 | 5.3221 | 12.027 | 116.5 | 0.04 Kspace | 4232.3 | 4652.7 | 4859.5 | 180.4 | 37.54 Neigh | 320.57 | 321.52 | 322.33 | 3.1 | 2.59 Comm | 708.51 | 725.52 | 739 | 25.2 | 5.85 Output | 0.0086096 | 0.010856 | 0.012952 | 1.3 | 0.00 Modify | 1473 | 1800.9 | 2163 | 655.4 | 14.53 Other | | 430.3 | | | 3.47 Nlocal: 284.406 ave 304 max 264 min Histogram: 1 4 1 4 3 7 6 2 1 3 Nghost: 4831.16 ave 4894 max 4756 min Histogram: 2 2 4 2 2 4 7 4 2 3 Neighs: 84457 ave 92586 max 77561 min Histogram: 3 4 3 2 6 5 5 1 0 3 Total # of neighbors = 2702623 Ave neighs/atom = 296.95891 Ave special neighs/atom = 1.8929788 Neighbor list builds = 102585 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) = 0.32612183 grid = 45 45 45 stencil order = 5 estimated absolute RMS force accuracy = 0.003112663 estimated relative force accuracy = 9.3736922e-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 0.969977 1.0894e-06 8304 2 103.7 8.95677e-05 2768 Per MPI rank memory allocation (min/avg/max) = 12.81 | 13.14 | 13.32 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 278.85094 97472.51 1.245531 291.97385 44.333427 82.808542 0 0 21466.082 89915.763 -427.18808 -272812.97 -161303.99 5510.8572 Loop time of 8.28056e-06 on 32 procs for 0 steps with 9101 atoms 114.0% 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 | | 8.281e-06 | | |100.00 Nlocal: 284.406 ave 304 max 264 min Histogram: 1 4 1 4 3 7 6 2 1 3 Nghost: 4831.16 ave 4894 max 4756 min Histogram: 2 2 4 2 2 4 7 4 2 3 Neighs: 84457 ave 92586 max 77561 min Histogram: 3 4 3 2 6 5 5 1 0 3 Total # of neighbors = 2702623 Ave neighs/atom = 296.95891 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: 6:37:24