#------------------------------------------------------------------------------- # 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 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 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) = 0.32729257 grid = 40 40 40 stencil order = 5 estimated absolute RMS force accuracy = 0.0030709373 estimated relative force accuracy = 9.2480364e-06 using double precision KISS FFT 3d grid and FFT values/proc = 7803 3200 generated 0 of 28 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.97 7.09655e-13 5784 2 103.7 7.70797e-11 1928 Per MPI rank memory allocation (min/avg/max) = 12.42 | 12.59 | 12.73 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 2788.0922 65360.011 1.3291045 304.39203 29.366107 35.462154 0 0 17244.339 55273.632 -321.48015 -198542.17 -125959.38 4044.8986 SHAKE stats (type/ave/delta/count) on step 50000 2 0.970058 1.10375e-06 5784 2 103.7 9.70368e-05 1928 SHAKE stats (type/ave/delta/count) on step 100000 2 0.970045 1.16126e-06 5784 2 103.7 9.10159e-05 1928 SHAKE stats (type/ave/delta/count) on step 150000 2 0.969952 1.20636e-06 5784 2 103.7 9.03642e-05 1928 SHAKE stats (type/ave/delta/count) on step 200000 2 0.969973 1.20914e-06 5784 2 103.7 0.000114442 1928 SHAKE stats (type/ave/delta/count) on step 250000 2 0.969969 1.21958e-06 5784 2 103.7 9.25464e-05 1928 SHAKE stats (type/ave/delta/count) on step 300000 2 0.969999 1.11835e-06 5784 2 103.7 9.0342e-05 1928 SHAKE stats (type/ave/delta/count) on step 350000 2 0.96995 1.18787e-06 5784 2 103.7 9.24625e-05 1928 SHAKE stats (type/ave/delta/count) on step 400000 2 0.969986 1.14095e-06 5784 2 103.7 0.000100711 1928 SHAKE stats (type/ave/delta/count) on step 450000 2 0.970037 1.91954e-06 5784 2 103.7 0.000160329 1928 SHAKE stats (type/ave/delta/count) on step 500000 2 0.970067 1.73419e-06 5784 2 103.7 0.000127355 1928 SHAKE stats (type/ave/delta/count) on step 550000 2 0.970005 1.35288e-06 5784 2 103.7 0.000101622 1928 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97002 9.97825e-07 5784 2 103.7 8.98794e-05 1928 SHAKE stats (type/ave/delta/count) on step 650000 2 0.970116 1.38429e-06 5784 2 103.7 0.000119295 1928 SHAKE stats (type/ave/delta/count) on step 700000 2 0.970049 1.12607e-06 5784 2 103.7 0.00010405 1928 SHAKE stats (type/ave/delta/count) on step 750000 2 0.969934 1.13726e-06 5784 2 103.7 0.000138085 1928 SHAKE stats (type/ave/delta/count) on step 800000 2 0.970023 1.61853e-06 5784 2 103.7 0.000101843 1928 SHAKE stats (type/ave/delta/count) on step 850000 2 0.969987 1.43167e-06 5784 2 103.7 9.1917e-05 1928 SHAKE stats (type/ave/delta/count) on step 900000 2 0.969915 1.52982e-06 5784 2 103.7 0.000113894 1928 SHAKE stats (type/ave/delta/count) on step 950000 2 0.970004 1.20236e-06 5784 2 103.7 9.0324e-05 1928 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.970007 1.28317e-06 5784 2 103.7 9.23914e-05 1928 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.969873 1.17842e-06 5784 2 103.7 9.46817e-05 1928 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.969964 1.16101e-06 5784 2 103.7 9.99474e-05 1928 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.969958 1.19937e-06 5784 2 103.7 0.000107942 1928 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97011 1.90349e-06 5784 2 103.7 0.000121859 1928 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.969999 1.34225e-06 5784 2 103.7 8.96183e-05 1928 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.969954 1.27038e-06 5784 2 103.7 9.49784e-05 1928 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.969989 1.28685e-06 5784 2 103.7 0.000117246 1928 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.969986 1.61627e-06 5784 2 103.7 0.000135362 1928 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.970062 1.22094e-06 5784 2 103.7 9.25745e-05 1928 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.970003 1.27765e-06 5784 2 103.7 9.98949e-05 1928 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.969879 1.2272e-06 5784 2 103.7 9.49991e-05 1928 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.970071 1.85625e-06 5784 2 103.7 0.000113335 1928 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.970011 1.78839e-06 5784 2 103.7 9.91619e-05 1928 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.969901 1.43633e-06 5784 2 103.7 0.000140836 1928 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.969917 1.47855e-06 5784 2 103.7 0.000119517 1928 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97015 2.20864e-06 5784 2 103.7 0.000151109 1928 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.970066 1.13158e-06 5784 2 103.7 9.25329e-05 1928 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97013 1.89973e-06 5784 2 103.7 0.000152991 1928 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.969939 1.52467e-06 5784 2 103.7 0.000107242 1928 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.970076 1.24714e-06 5784 2 103.7 9.44799e-05 1928 2000000 2000000 -446.21926 69068.325 1.2577442 301.16034 28.445158 42.026347 0 0 16252.823 56543.181 -304.21971 -198507.07 -125640.6 4001.9545 Loop time of 9205.06 on 32 procs for 2000000 steps with 6387 atoms Performance: 18.772 ns/day, 1.278 hours/ns, 217.272 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 | 3035.3 | 3249.6 | 3597.9 | 233.9 | 35.30 Bond | 1.9344 | 4.0464 | 8.2727 | 93.8 | 0.04 Kspace | 2987.1 | 3342.9 | 3557.8 | 232.3 | 36.32 Neigh | 201.23 | 201.62 | 201.94 | 1.6 | 2.19 Comm | 591.41 | 601.97 | 610.38 | 18.0 | 6.54 Output | 0.0079208 | 0.0097512 | 0.011487 | 1.1 | 0.00 Modify | 1160.6 | 1357.5 | 1757.7 | 577.7 | 14.75 Other | | 447.3 | | | 4.86 Nlocal: 199.594 ave 219 max 177 min Histogram: 1 2 1 4 5 7 4 5 1 2 Nghost: 4255.59 ave 4300 max 4212 min Histogram: 1 3 3 4 6 3 6 2 3 1 Neighs: 58709.8 ave 65339 max 50351 min Histogram: 1 1 3 5 5 3 5 2 2 5 Total # of neighbors = 1878713 Ave neighs/atom = 294.14639 Ave special neighs/atom = 1.8738062 Neighbor list builds = 99596 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) = 0.32590203 grid = 40 40 40 stencil order = 5 estimated absolute RMS force accuracy = 0.0032435545 estimated relative force accuracy = 9.7678681e-06 using double precision KISS FFT 3d grid and FFT values/proc = 7803 3200 generated 0 of 28 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 2 0.970076 1.24714e-06 5784 2 103.7 9.44799e-05 1928 Per MPI rank memory allocation (min/avg/max) = 12.42 | 12.61 | 12.73 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 -9.6066933 69068.325 1.2577442 301.16034 28.445158 42.026347 0 0 16252.823 55718.531 -304.21971 -197682.43 -125640.6 4001.9545 Loop time of 8.06625e-06 on 32 procs for 0 steps with 6387 atoms 104.2% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 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 | | 8.066e-06 | | |100.00 Nlocal: 199.594 ave 219 max 177 min Histogram: 1 2 1 4 5 7 4 5 1 2 Nghost: 4255.59 ave 4300 max 4212 min Histogram: 1 3 3 4 6 3 6 2 3 1 Neighs: 58709.8 ave 65339 max 50351 min Histogram: 1 1 3 5 5 3 5 2 2 5 Total # of neighbors = 1878713 Ave neighs/atom = 294.14639 Ave special neighs/atom = 1.8738062 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken Total wall time: 4:49:41