#------------------------------------------------------------------------------- # Stage 2.4: NPT integration for 200 ps with a timestep of 0.1 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 8303 = # of frozen angles find clusters CPU = 0.002 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 2.4_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_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 2.4_instantaneous.txt restart 2000000 2.4.restart dump sci all custom 200000 2.4.xyz id mol type q xs ys zs timestep 0.1 run 2000000 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.994608 0.973045 24909 2 96.7496 67.809 8303 Per MPI rank memory allocation (min/avg/max) = 12.57 | 12.61 | 12.77 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 23016.402 278556.86 1.3074059 428.54084 1527.3359 984.67987 0 0 79401.614 -500633.7 -1345.0391 0 -418720.07 24265.468 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 7.68519e-09 24909 2 103.7 4.44123e-07 8303 SHAKE stats (type/ave/delta/count) on step 100000 2 0.969998 6.25807e-09 24909 2 103.7 5.54425e-07 8303 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 5.9278e-09 24909 2 103.7 4.9075e-07 8303 SHAKE stats (type/ave/delta/count) on step 200000 2 0.970003 7.1018e-09 24909 2 103.7 5.67303e-07 8303 SHAKE stats (type/ave/delta/count) on step 250000 2 0.969999 6.79538e-09 24909 2 103.7 5.54488e-07 8303 SHAKE stats (type/ave/delta/count) on step 300000 2 0.969999 7.16521e-09 24909 2 103.7 5.54194e-07 8303 SHAKE stats (type/ave/delta/count) on step 350000 2 0.969998 6.20573e-09 24909 2 103.7 4.98884e-07 8303 SHAKE stats (type/ave/delta/count) on step 400000 2 0.969997 7.37335e-09 24909 2 103.7 5.51976e-07 8303 SHAKE stats (type/ave/delta/count) on step 450000 2 0.96999 6.86896e-09 24909 2 103.7 4.88487e-07 8303 SHAKE stats (type/ave/delta/count) on step 500000 2 0.969994 6.95221e-09 24909 2 103.7 4.22172e-07 8303 SHAKE stats (type/ave/delta/count) on step 550000 2 0.970005 6.76769e-09 24909 2 103.7 3.99777e-07 8303 SHAKE stats (type/ave/delta/count) on step 600000 2 0.970002 7.23479e-09 24909 2 103.7 4.2796e-07 8303 SHAKE stats (type/ave/delta/count) on step 650000 2 0.970003 6.71948e-09 24909 2 103.7 4.78664e-07 8303 SHAKE stats (type/ave/delta/count) on step 700000 2 0.969998 6.77399e-09 24909 2 103.7 4.19352e-07 8303 SHAKE stats (type/ave/delta/count) on step 750000 2 0.969997 7.20412e-09 24909 2 103.7 4.3571e-07 8303 SHAKE stats (type/ave/delta/count) on step 800000 2 0.969996 7.15173e-09 24909 2 103.7 4.392e-07 8303 SHAKE stats (type/ave/delta/count) on step 850000 2 0.970006 6.61754e-09 24909 2 103.7 3.8026e-07 8303 SHAKE stats (type/ave/delta/count) on step 900000 2 0.970004 7.48968e-09 24909 2 103.7 4.57124e-07 8303 SHAKE stats (type/ave/delta/count) on step 950000 2 0.969994 6.30214e-09 24909 2 103.7 4.61189e-07 8303 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.970003 6.86977e-09 24909 2 103.7 4.8564e-07 8303 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.969998 6.07183e-09 24909 2 103.7 4.90017e-07 8303 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.970001 7.26101e-09 24909 2 103.7 5.40852e-07 8303 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.970006 6.27212e-09 24909 2 103.7 4.22576e-07 8303 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.969997 7.59891e-09 24909 2 103.7 4.72094e-07 8303 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.00369e-08 24909 2 103.7 6.73756e-07 8303 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.970005 6.00941e-09 24909 2 103.7 4.06302e-07 8303 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.970007 6.43593e-09 24909 2 103.7 3.54606e-07 8303 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.969998 6.27201e-09 24909 2 103.7 3.86981e-07 8303 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.970002 5.84989e-09 24909 2 103.7 4.12898e-07 8303 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.970002 6.79401e-09 24909 2 103.7 3.88708e-07 8303 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.970009 8.184e-09 24909 2 103.7 5.05992e-07 8303 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.970003 8.25104e-09 24909 2 103.7 5.17278e-07 8303 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.969999 6.35769e-09 24909 2 103.7 4.39397e-07 8303 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 6.26099e-09 24909 2 103.7 4.44808e-07 8303 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.970002 6.27567e-09 24909 2 103.7 4.76803e-07 8303 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.970001 6.69064e-09 24909 2 103.7 4.74407e-07 8303 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.969998 6.31502e-09 24909 2 103.7 4.82893e-07 8303 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.970006 6.72411e-09 24909 2 103.7 5.10616e-07 8303 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.969995 6.89858e-09 24909 2 103.7 4.57167e-07 8303 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.970003 7.15799e-09 24909 2 103.7 5.85085e-07 8303 2000000 200000 654.10411 297622.26 1.2236547 294.37026 123.42346 391.29778 0 0 59603.332 -474418.44 -1258.8771 0 -414300.39 16668.265 Loop time of 13964.7 on 32 procs for 2000000 steps with 27300 atoms Performance: 1.237 ns/day, 19.395 hours/ns, 143.219 timesteps/s 99.5% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 10595 | 11488 | 12079 | 344.3 | 82.26 Bond | 2.5564 | 9.3705 | 14.273 | 84.9 | 0.07 Neigh | 77.16 | 77.315 | 77.499 | 1.3 | 0.55 Comm | 628.64 | 1232.6 | 2147.7 |1114.9 | 8.83 Output | 0.022065 | 0.027001 | 0.031743 | 1.8 | 0.00 Modify | 1047.6 | 1110.5 | 1196.6 | 138.7 | 7.95 Other | | 47.24 | | | 0.34 Nlocal: 853.125 ave 882 max 809 min Histogram: 1 1 3 1 0 6 11 5 2 2 Nghost: 6985.56 ave 7058 max 6922 min Histogram: 2 1 6 2 7 6 3 2 1 2 Neighs: 247925 ave 260277 max 228040 min Histogram: 1 2 3 0 1 7 7 3 5 3 Total # of neighbors = 7933611 Ave neighs/atom = 290.60846 Ave special neighs/atom = 1.892967 Neighbor list builds = 10951 Dangerous builds = 0 undump sci restart 0 dump sci all custom 2000000 2.4.xyz id mol type q xs ys zs run 0 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 2 0.970003 7.15799e-09 24909 2 103.7 5.85085e-07 8303 Per MPI rank memory allocation (min/avg/max) = 12.57 | 12.62 | 12.77 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 200000 2100.8542 297622.26 1.2236547 294.37026 123.42346 391.29778 0 0 59603.332 -474418.44 -1258.8771 0 -414300.39 16668.265 Loop time of 7.16947e-06 on 32 procs for 0 steps with 27300 atoms 113.8% 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 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 | | 7.169e-06 | | |100.00 Nlocal: 853.125 ave 882 max 809 min Histogram: 1 1 3 1 0 6 11 5 2 2 Nghost: 6985.56 ave 7058 max 6922 min Histogram: 2 1 6 2 7 6 3 2 1 2 Neighs: 247925 ave 260277 max 228040 min Histogram: 1 2 3 0 1 7 7 3 5 3 Total # of neighbors = 7933611 Ave neighs/atom = 290.60846 Ave special neighs/atom = 1.892967 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken log 2.5_NVT.out