#------------------------------------------------------------------------------- # Stage 2.4: NPT integration for 5 ns with a timestep of 1 fs # Temperature 298.15 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 298.15 298.15 100 iso 1 1 100 drag 0 mtk yes nreset 100000 fix 2 movable ave/time 1 499999 500000 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 500 1 500 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 5000000 2.4.restart dump sci all custom 500000 2.4.xyz id mol type q xs ys zs timestep 1 run 5000000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.32489129 grid = 72 72 48 stencil order = 5 estimated absolute RMS force accuracy = 0.0034280733 estimated relative force accuracy = 1.0323541e-05 using double precision KISS FFT 3d grid and FFT values/proc = 19375 10368 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.992518 1.12928 24909 2 96.605 63.2761 8303 Per MPI rank memory allocation (min/avg/max) = 14.37 | 14.54 | 15.01 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 26935.081 278556.86 1.3074059 428.46899 571.12129 1095.4738 0 0 83132.65 318013.41 -1345.0391 -800663.24 -397850.59 24261.4 SHAKE stats (type/ave/delta/count) on step 50000 2 0.969984 1.09995e-06 24909 2 103.7 0.000107221 8303 SHAKE stats (type/ave/delta/count) on step 100000 2 0.96998 1.28289e-06 24909 2 103.7 0.000100635 8303 SHAKE stats (type/ave/delta/count) on step 150000 2 0.969982 1.20793e-06 24909 2 103.7 0.000101219 8303 SHAKE stats (type/ave/delta/count) on step 200000 2 0.969947 1.34168e-06 24909 2 103.7 9.33464e-05 8303 SHAKE stats (type/ave/delta/count) on step 250000 2 0.970024 1.46783e-06 24909 2 103.7 0.00010246 8303 SHAKE stats (type/ave/delta/count) on step 300000 2 0.970036 1.29055e-06 24909 2 103.7 9.91908e-05 8303 SHAKE stats (type/ave/delta/count) on step 350000 2 0.970039 1.71957e-06 24909 2 103.7 0.000104781 8303 SHAKE stats (type/ave/delta/count) on step 400000 2 0.969975 1.44068e-06 24909 2 103.7 0.000114798 8303 SHAKE stats (type/ave/delta/count) on step 450000 2 0.970009 1.43982e-06 24909 2 103.7 0.000107121 8303 SHAKE stats (type/ave/delta/count) on step 500000 2 0.970006 1.59491e-06 24909 2 103.7 0.000122524 8303 SHAKE stats (type/ave/delta/count) on step 550000 2 0.970026 1.29657e-06 24909 2 103.7 9.38977e-05 8303 SHAKE stats (type/ave/delta/count) on step 600000 2 0.969993 1.53506e-06 24909 2 103.7 0.000110526 8303 SHAKE stats (type/ave/delta/count) on step 650000 2 0.969967 1.28967e-06 24909 2 103.7 9.53913e-05 8303 SHAKE stats (type/ave/delta/count) on step 700000 2 0.969986 1.49805e-06 24909 2 103.7 0.000105539 8303 SHAKE stats (type/ave/delta/count) on step 750000 2 0.96998 1.23526e-06 24909 2 103.7 0.000105554 8303 SHAKE stats (type/ave/delta/count) on step 800000 2 0.970019 1.45675e-06 24909 2 103.7 9.46814e-05 8303 SHAKE stats (type/ave/delta/count) on step 850000 2 0.96995 1.19764e-06 24909 2 103.7 0.000107782 8303 SHAKE stats (type/ave/delta/count) on step 900000 2 0.969979 1.24958e-06 24909 2 103.7 9.85714e-05 8303 SHAKE stats (type/ave/delta/count) on step 950000 2 0.96999 1.13858e-06 24909 2 103.7 0.000103617 8303 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.969987 1.51585e-06 24909 2 103.7 0.000108437 8303 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.970059 1.81266e-06 24909 2 103.7 0.000123062 8303 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.970054 1.84645e-06 24909 2 103.7 0.000122687 8303 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.969978 1.14689e-06 24909 2 103.7 9.93589e-05 8303 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.970004 1.37147e-06 24909 2 103.7 0.000107475 8303 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97001 1.43099e-06 24909 2 103.7 9.86692e-05 8303 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.970037 1.32295e-06 24909 2 103.7 0.000108397 8303 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.970032 1.35043e-06 24909 2 103.7 0.000106901 8303 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.969969 1.64762e-06 24909 2 103.7 0.000101666 8303 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.969973 1.2763e-06 24909 2 103.7 9.24753e-05 8303 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97001 1.51674e-06 24909 2 103.7 9.90925e-05 8303 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.969979 1.34461e-06 24909 2 103.7 9.77108e-05 8303 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.26863e-06 24909 2 103.7 9.767e-05 8303 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.969994 1.21762e-06 24909 2 103.7 0.0001063 8303 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.969935 1.46409e-06 24909 2 103.7 0.000108538 8303 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.969964 1.73014e-06 24909 2 103.7 0.000113367 8303 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.19698e-06 24909 2 103.7 9.64972e-05 8303 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.969982 1.22932e-06 24909 2 103.7 9.69656e-05 8303 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.969991 1.29711e-06 24909 2 103.7 0.000113092 8303 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.970016 1.33345e-06 24909 2 103.7 9.61582e-05 8303 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.970009 1.22941e-06 24909 2 103.7 0.000103206 8303 SHAKE stats (type/ave/delta/count) on step 2050000 2 0.969992 1.19606e-06 24909 2 103.7 0.000103236 8303 SHAKE stats (type/ave/delta/count) on step 2100000 2 0.970004 1.38781e-06 24909 2 103.7 0.000119788 8303 SHAKE stats (type/ave/delta/count) on step 2150000 2 0.969946 1.4405e-06 24909 2 103.7 0.000106518 8303 SHAKE stats (type/ave/delta/count) on step 2200000 2 0.969997 1.19826e-06 24909 2 103.7 9.77991e-05 8303 SHAKE stats (type/ave/delta/count) on step 2250000 2 0.969978 1.34499e-06 24909 2 103.7 0.000114878 8303 SHAKE stats (type/ave/delta/count) on step 2300000 2 0.969957 1.31972e-06 24909 2 103.7 9.72116e-05 8303 SHAKE stats (type/ave/delta/count) on step 2350000 2 0.970024 1.48553e-06 24909 2 103.7 0.000110638 8303 SHAKE stats (type/ave/delta/count) on step 2400000 2 0.970011 1.39991e-06 24909 2 103.7 0.000109693 8303 SHAKE stats (type/ave/delta/count) on step 2450000 2 0.97001 1.2978e-06 24909 2 103.7 0.000103369 8303 SHAKE stats (type/ave/delta/count) on step 2500000 2 0.970007 1.41848e-06 24909 2 103.7 0.000107285 8303 SHAKE stats (type/ave/delta/count) on step 2550000 2 0.969919 1.41194e-06 24909 2 103.7 0.000119235 8303 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.969962 1.41882e-06 24909 2 103.7 0.000112693 8303 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.969972 1.3408e-06 24909 2 103.7 0.000111207 8303 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.969997 1.1534e-06 24909 2 103.7 0.000107121 8303 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.970002 1.41487e-06 24909 2 103.7 9.95846e-05 8303 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.969985 1.3883e-06 24909 2 103.7 0.000105402 8303 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.970001 1.42934e-06 24909 2 103.7 0.000105963 8303 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.970022 1.23569e-06 24909 2 103.7 0.000109671 8303 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.969992 1.38552e-06 24909 2 103.7 0.000100432 8303 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.969967 1.38444e-06 24909 2 103.7 0.000127514 8303 SHAKE stats (type/ave/delta/count) on step 3050000 2 0.970003 1.28422e-06 24909 2 103.7 0.000106865 8303 SHAKE stats (type/ave/delta/count) on step 3100000 2 0.97001 1.88878e-06 24909 2 103.7 0.000122255 8303 SHAKE stats (type/ave/delta/count) on step 3150000 2 0.97 1.2297e-06 24909 2 103.7 0.000100688 8303 SHAKE stats (type/ave/delta/count) on step 3200000 2 0.969997 1.37152e-06 24909 2 103.7 9.74375e-05 8303 SHAKE stats (type/ave/delta/count) on step 3250000 2 0.970004 1.53259e-06 24909 2 103.7 9.42999e-05 8303 SHAKE stats (type/ave/delta/count) on step 3300000 2 0.970032 1.35745e-06 24909 2 103.7 9.56332e-05 8303 SHAKE stats (type/ave/delta/count) on step 3350000 2 0.970054 1.1741e-06 24909 2 103.7 9.57536e-05 8303 SHAKE stats (type/ave/delta/count) on step 3400000 2 0.970044 1.486e-06 24909 2 103.7 0.000108877 8303 SHAKE stats (type/ave/delta/count) on step 3450000 2 0.96998 1.44202e-06 24909 2 103.7 0.000104602 8303 SHAKE stats (type/ave/delta/count) on step 3500000 2 0.970007 1.40172e-06 24909 2 103.7 0.000102078 8303 SHAKE stats (type/ave/delta/count) on step 3550000 2 0.970021 1.50229e-06 24909 2 103.7 9.95192e-05 8303 SHAKE stats (type/ave/delta/count) on step 3600000 2 0.969997 1.34961e-06 24909 2 103.7 0.000106631 8303 SHAKE stats (type/ave/delta/count) on step 3650000 2 0.969982 1.35612e-06 24909 2 103.7 0.000104702 8303 SHAKE stats (type/ave/delta/count) on step 3700000 2 0.970011 1.32861e-06 24909 2 103.7 0.000103392 8303 SHAKE stats (type/ave/delta/count) on step 3750000 2 0.970015 1.47364e-06 24909 2 103.7 0.000114833 8303 SHAKE stats (type/ave/delta/count) on step 3800000 2 0.97006 1.33509e-06 24909 2 103.7 9.73229e-05 8303 SHAKE stats (type/ave/delta/count) on step 3850000 2 0.970047 1.5001e-06 24909 2 103.7 0.000122192 8303 SHAKE stats (type/ave/delta/count) on step 3900000 2 0.969979 1.23108e-06 24909 2 103.7 0.00010004 8303 SHAKE stats (type/ave/delta/count) on step 3950000 2 0.969977 1.30687e-06 24909 2 103.7 0.000110102 8303 SHAKE stats (type/ave/delta/count) on step 4000000 2 0.970013 1.61353e-06 24909 2 103.7 0.000109657 8303 SHAKE stats (type/ave/delta/count) on step 4050000 2 0.970035 1.24115e-06 24909 2 103.7 9.42218e-05 8303 SHAKE stats (type/ave/delta/count) on step 4100000 2 0.970042 1.19613e-06 24909 2 103.7 9.43222e-05 8303 SHAKE stats (type/ave/delta/count) on step 4150000 2 0.969972 1.61058e-06 24909 2 103.7 0.000102122 8303 SHAKE stats (type/ave/delta/count) on step 4200000 2 0.970045 1.51888e-06 24909 2 103.7 0.000113559 8303 SHAKE stats (type/ave/delta/count) on step 4250000 2 0.969954 1.37448e-06 24909 2 103.7 0.000104581 8303 SHAKE stats (type/ave/delta/count) on step 4300000 2 0.969954 1.429e-06 24909 2 103.7 9.9604e-05 8303 SHAKE stats (type/ave/delta/count) on step 4350000 2 0.970039 1.54609e-06 24909 2 103.7 0.000109789 8303 SHAKE stats (type/ave/delta/count) on step 4400000 2 0.970064 1.79838e-06 24909 2 103.7 0.000135425 8303 SHAKE stats (type/ave/delta/count) on step 4450000 2 0.970002 1.27236e-06 24909 2 103.7 0.00010594 8303 SHAKE stats (type/ave/delta/count) on step 4500000 2 0.970006 1.18058e-06 24909 2 103.7 9.65772e-05 8303 SHAKE stats (type/ave/delta/count) on step 4550000 2 0.969983 1.33843e-06 24909 2 103.7 9.98336e-05 8303 SHAKE stats (type/ave/delta/count) on step 4600000 2 0.970037 1.54633e-06 24909 2 103.7 0.000104021 8303 SHAKE stats (type/ave/delta/count) on step 4650000 2 0.969962 1.36678e-06 24909 2 103.7 9.82244e-05 8303 SHAKE stats (type/ave/delta/count) on step 4700000 2 0.970015 1.18651e-06 24909 2 103.7 0.000106886 8303 SHAKE stats (type/ave/delta/count) on step 4750000 2 0.969954 1.44817e-06 24909 2 103.7 0.000112082 8303 SHAKE stats (type/ave/delta/count) on step 4800000 2 0.970014 1.31955e-06 24909 2 103.7 9.929e-05 8303 SHAKE stats (type/ave/delta/count) on step 4850000 2 0.970005 1.44736e-06 24909 2 103.7 0.000103657 8303 SHAKE stats (type/ave/delta/count) on step 4900000 2 0.970055 1.60462e-06 24909 2 103.7 0.000110708 8303 SHAKE stats (type/ave/delta/count) on step 4950000 2 0.969984 1.2699e-06 24909 2 103.7 9.66531e-05 8303 SHAKE stats (type/ave/delta/count) on step 5000000 2 0.969976 1.21066e-06 24909 2 103.7 0.000111239 8303 5000000 5000000 -138.65793 292264.88 1.246085 303.02714 136.79195 200.01694 0 0 63275.384 267790.38 -1281.9531 -814999.08 -483596.51 17158.447 Loop time of 80852 on 32 procs for 5000000 steps with 27300 atoms Performance: 5.343 ns/day, 4.492 hours/ns, 61.841 timesteps/s 99.3% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 30418 | 31789 | 33078 | 351.2 | 39.32 Bond | 16.624 | 28.139 | 54.644 | 139.9 | 0.03 Kspace | 29728 | 31025 | 32325 | 355.3 | 38.37 Neigh | 2089.3 | 2093.5 | 2096.4 | 3.9 | 2.59 Comm | 3648.4 | 3702.6 | 3765 | 56.1 | 4.58 Output | 0.022483 | 0.027324 | 0.03198 | 1.7 | 0.00 Modify | 8033.7 | 10027 | 11852 |1687.5 | 12.40 Other | | 2187 | | | 2.71 Nlocal: 853.125 ave 896 max 823 min Histogram: 1 5 4 7 6 3 3 0 0 3 Nghost: 7078.66 ave 7132 max 7022 min Histogram: 1 2 3 4 7 3 4 1 5 2 Neighs: 253484 ave 270618 max 240812 min Histogram: 2 7 2 6 3 5 1 3 1 2 Total # of neighbors = 8111492 Ave neighs/atom = 297.12425 Ave special neighs/atom = 1.892967 Neighbor list builds = 277428 Dangerous builds = 1 undump sci restart 0 dump sci all custom 5000000 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) = 0.32366646 grid = 72 72 48 stencil order = 5 estimated absolute RMS force accuracy = 0.0035958189 estimated relative force accuracy = 1.0828702e-05 using double precision KISS FFT 3d grid and FFT values/proc = 19375 10368 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 5000000 2 0.969976 1.21066e-06 24909 2 103.7 0.000111239 8303 Per MPI rank memory allocation (min/avg/max) = 14.37 | 14.62 | 15.01 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 5000000 5000000 -280.12513 292264.88 1.246085 303.02714 136.79195 200.01694 0 0 63275.384 264779.82 -1281.9531 -811988.53 -483596.51 17158.447 Loop time of 1.15843e-05 on 32 procs for 0 steps with 27300 atoms 107.6% 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 | | 1.158e-05 | | |100.00 Nlocal: 853.125 ave 896 max 823 min Histogram: 1 5 4 7 6 3 3 0 0 3 Nghost: 7078.66 ave 7132 max 7022 min Histogram: 1 2 3 4 7 3 4 1 5 2 Neighs: 253484 ave 270618 max 240812 min Histogram: 2 7 2 6 3 5 1 3 1 2 Total # of neighbors = 8111492 Ave neighs/atom = 297.12425 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