#------------------------------------------------------------------------------- # Stage 2.4: NVT integration for 3 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 300000 300000 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 300 1 300 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 3000000 2.4.restart dump sci all custom 300000 2.4.xyz id mol type q xs ys zs timestep 1 run 3000000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.25049777 grid = 30 30 50 stencil order = 5 estimated absolute RMS force accuracy = 0.0035336797 estimated relative force accuracy = 1.0641571e-05 using double precision KISS FFT 3d grid and FFT values/proc = 6292 1800 generated 0 of 28 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 1.0016 0.0759118 5784 2 97.5148 10.5518 1928 Per MPI rank memory allocation (min/avg/max) = 10.94 | 12.3 | 13.54 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-06 208.51845 138406.7 0.6276451 427.16581 5.9499764 13.59042 0 0 19657.178 -2164.871 -76.429471 -152468.77 -134956.92 5676.3721 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.30386e-06 5784 2 103.7 9.88569e-05 1928 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.11729e-06 5784 2 103.7 0.000118595 1928 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.25969e-06 5784 2 103.7 9.45221e-05 1928 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.14998e-06 5784 2 103.7 0.000100423 1928 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.25051e-06 5784 2 103.7 9.38168e-05 1928 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.19574e-06 5784 2 103.7 0.000108702 1928 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.68029e-06 5784 2 103.7 0.000100934 1928 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.56312e-06 5784 2 103.7 0.000106144 1928 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.49596e-06 5784 2 103.7 0.000109754 1928 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.15747e-06 5784 2 103.7 9.07033e-05 1928 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.14823e-06 5784 2 103.7 9.67862e-05 1928 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.14694e-06 5784 2 103.7 9.90589e-05 1928 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.21113e-06 5784 2 103.7 8.88731e-05 1928 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.2062e-06 5784 2 103.7 9.07005e-05 1928 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.36445e-06 5784 2 103.7 9.34534e-05 1928 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.18027e-06 5784 2 103.7 0.000101239 1928 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.7111e-06 5784 2 103.7 0.000129902 1928 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.48188e-06 5784 2 103.7 0.000118869 1928 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.06486e-06 5784 2 103.7 9.6164e-05 1928 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.38122e-06 5784 2 103.7 0.000111534 1928 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.19964e-06 5784 2 103.7 9.34377e-05 1928 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.19017e-06 5784 2 103.7 9.28035e-05 1928 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.24441e-06 5784 2 103.7 9.21238e-05 1928 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.29321e-06 5784 2 103.7 8.56554e-05 1928 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.53285e-06 5784 2 103.7 0.000131333 1928 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.09291e-06 5784 2 103.7 9.16428e-05 1928 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.13985e-06 5784 2 103.7 9.74529e-05 1928 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.04307e-06 5784 2 103.7 0.00010238 1928 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.17337e-06 5784 2 103.7 0.000112033 1928 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.41595e-06 5784 2 103.7 9.93321e-05 1928 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.31106e-06 5784 2 103.7 0.000112545 1928 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.30044e-06 5784 2 103.7 0.000103736 1928 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.27361e-06 5784 2 103.7 9.79187e-05 1928 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.50942e-06 5784 2 103.7 0.000102 1928 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.60202e-06 5784 2 103.7 0.000133064 1928 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.19858e-06 5784 2 103.7 0.000110497 1928 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.08311e-06 5784 2 103.7 8.63459e-05 1928 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.17901e-06 5784 2 103.7 9.75825e-05 1928 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.23583e-06 5784 2 103.7 9.52909e-05 1928 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.64937e-06 5784 2 103.7 0.000129647 1928 SHAKE stats (type/ave/delta/count) on step 2050000 2 0.97 1.14066e-06 5784 2 103.7 9.89928e-05 1928 SHAKE stats (type/ave/delta/count) on step 2100000 2 0.97 1.09787e-06 5784 2 103.7 0.000114629 1928 SHAKE stats (type/ave/delta/count) on step 2150000 2 0.97 1.38113e-06 5784 2 103.7 9.77533e-05 1928 SHAKE stats (type/ave/delta/count) on step 2200000 2 0.97 1.13883e-06 5784 2 103.7 0.000104826 1928 SHAKE stats (type/ave/delta/count) on step 2250000 2 0.97 1.39108e-06 5784 2 103.7 0.000113321 1928 SHAKE stats (type/ave/delta/count) on step 2300000 2 0.97 1.55797e-06 5784 2 103.7 0.000111734 1928 SHAKE stats (type/ave/delta/count) on step 2350000 2 0.97 1.18979e-06 5784 2 103.7 9.49676e-05 1928 SHAKE stats (type/ave/delta/count) on step 2400000 2 0.97 1.57452e-06 5784 2 103.7 0.000107347 1928 SHAKE stats (type/ave/delta/count) on step 2450000 2 0.97 2.15552e-06 5784 2 103.7 0.00014618 1928 SHAKE stats (type/ave/delta/count) on step 2500000 2 0.97 1.75246e-06 5784 2 103.7 0.000140252 1928 SHAKE stats (type/ave/delta/count) on step 2550000 2 0.97 1.28606e-06 5784 2 103.7 0.000109282 1928 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.97 1.18253e-06 5784 2 103.7 8.81696e-05 1928 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.97 1.79926e-06 5784 2 103.7 0.000150385 1928 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.97 1.29931e-06 5784 2 103.7 8.85179e-05 1928 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.97 1.16053e-06 5784 2 103.7 9.38525e-05 1928 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.97 1.31688e-06 5784 2 103.7 0.000104372 1928 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.97 1.11137e-06 5784 2 103.7 0.000113854 1928 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.97 1.09462e-06 5784 2 103.7 9.75767e-05 1928 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.97 1.40339e-06 5784 2 103.7 0.000117865 1928 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.08911e-06 5784 2 103.7 9.83036e-05 1928 3000000 3000000 -182.33582 138406.7 0.6276451 294.86076 28.288073 33.066383 0 0 16268.863 11311.319 -76.429471 -152461.48 -124819.95 3918.2428 Loop time of 25554 on 32 procs for 3000000 steps with 6387 atoms Performance: 10.143 ns/day, 2.366 hours/ns, 117.398 timesteps/s 98.4% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.2572 | 7732.5 | 18236 |8567.1 | 30.26 Bond | 2.7146 | 5.739 | 13.855 | 129.5 | 0.02 Kspace | 4208.9 | 14766 | 22660 |6243.0 | 57.78 Neigh | 1247.6 | 1254.2 | 1265 | 16.3 | 4.91 Comm | 229.3 | 641.24 | 883.35 | 911.8 | 2.51 Output | 0.011618 | 0.013439 | 0.015053 | 0.9 | 0.00 Modify | 932.65 | 1108.4 | 1349 | 495.5 | 4.34 Other | | 45.48 | | | 0.18 Nlocal: 199.594 ave 406 max 0 min Histogram: 12 0 0 4 0 0 3 1 0 12 Nghost: 3927.66 ave 7680 max 100 min Histogram: 4 4 4 0 4 4 0 4 4 4 Neighs: 90950.7 ave 221313 max 0 min Histogram: 16 0 0 0 0 2 2 3 4 5 Total # of neighbors = 2910422 Ave neighs/atom = 455.67904 Ave special neighs/atom = 1.8738062 Neighbor list builds = 145124 Dangerous builds = 0 undump sci restart 0 dump sci all custom 3000000 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) = 0.25049777 grid = 30 30 50 stencil order = 5 estimated absolute RMS force accuracy = 0.0035336797 estimated relative force accuracy = 1.0641571e-05 using double precision KISS FFT 3d grid and FFT values/proc = 6292 1800 generated 0 of 28 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.08911e-06 5784 2 103.7 9.83036e-05 1928 Per MPI rank memory allocation (min/avg/max) = 11.07 | 12.42 | 13.54 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 3000000 3000000 -181.86694 138406.7 0.6276451 294.86076 28.288073 33.066383 0 0 16268.863 11311.319 -76.429471 -152461.48 -124819.95 3918.2428 Loop time of 1.35677e-05 on 32 procs for 0 steps with 6387 atoms 106.9% 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 | | 1.357e-05 | | |100.00 Nlocal: 199.594 ave 406 max 0 min Histogram: 12 0 0 4 0 0 3 1 0 12 Nghost: 3927.66 ave 7680 max 100 min Histogram: 4 4 4 0 4 4 0 4 4 4 Neighs: 90950.7 ave 221313 max 0 min Histogram: 16 0 0 0 0 2 2 3 4 5 Total # of neighbors = 2910422 Ave neighs/atom = 455.67904 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_NVT.out