#------------------------------------------------------------------------------- # Stage 2.4: NPT integration for 2 ns with a timestep of 1 fs # Temperature 298.2 K # Pressure 1 bar #------------------------------------------------------------------------------- # 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 = 0.002 seconds change_box all triclinic Changing box ... triclinic box = (0 0 0) to (35.89352 35.89352 72.07658) with tilt (0 0 0) kspace_style pppm 0.00001 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 change_box all triclinic Changing box ... triclinic box = (0 0 0) to (35.89352 35.89352 72.07658) with tilt (0 0 0) fix 1 movable npt temp 298.2 298.2 100 z 0.9869233 0.9869233 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 1 run 2000000 PPPM initialization ... WARNING: System is not charge neutral, net charge = 0.0206 (../kspace.cpp:325) using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.25787546 grid = 30 30 48 stencil order = 5 estimated absolute RMS force accuracy = 0.002900781 estimated relative force accuracy = 8.7356158e-06 using double precision KISS FFT 3d grid and FFT values/proc = 6292 1800 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 14 ghost atom cutoff = 14 binsize = 7, bins = 6 6 11 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair lj/class2/coul/long, perpetual attributes: half, newton on pair build: half/bin/newton/tri stencil: half/bin/3d/tri bin: standard SHAKE stats (type/ave/delta/count) on step 0 2 0.993721 0.838108 8304 2 96.7906 54.4205 2768 Per MPI rank memory allocation (min/avg/max) = 12.85 | 12.95 | 13.12 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 33929.375 92859.485 1.3074059 428.55654 116.30759 354.30891 0 0 28780.831 58369.616 -225.64506 -212596.4 -124975.34 8088.7858 SHAKE stats (type/ave/delta/count) on step 50000 2 0.969972 8.61244e-05 8304 2 103.7 0.00983828 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.969989 3.4365e-05 8304 2 103.7 0.00387411 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.970049 0.000146359 8304 2 103.7 0.0167588 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.969961 0.000120249 8304 2 103.7 0.0136738 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.96999 3.14211e-05 8304 2 103.7 0.0035259 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.970021 6.25412e-05 8304 2 103.7 0.00714447 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.970018 5.56235e-05 8304 2 103.7 0.00635637 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 2.46107e-06 8304 2 103.7 0.000241011 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.969982 5.48326e-05 8304 2 103.7 0.00623347 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.969994 1.98723e-05 8304 2 103.7 0.0022495 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.969958 0.000126965 8304 2 103.7 0.0144661 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.969968 9.70697e-05 8304 2 103.7 0.0110801 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.970006 1.94446e-05 8304 2 103.7 0.00221454 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.969992 2.62248e-05 8304 2 103.7 0.00297543 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.47413e-06 8304 2 103.7 0.000145934 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.970037 0.000111639 8304 2 103.7 0.012831 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.970053 0.000160436 8304 2 103.7 0.0183745 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.969996 1.38837e-05 8304 2 103.7 0.0015164 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.969972 8.44944e-05 8304 2 103.7 0.00963559 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.969985 4.56215e-05 8304 2 103.7 0.00513453 2768 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.970025 7.63675e-05 8304 2 103.7 0.00871117 2768 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.970037 0.000112525 8304 2 103.7 0.0128084 2768 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.970032 9.6906e-05 8304 2 103.7 0.0111142 2768 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.96997 9.32283e-05 8304 2 103.7 0.0105863 2768 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.969977 7.00722e-05 8304 2 103.7 0.00795148 2768 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.969971 8.74562e-05 8304 2 103.7 0.00995607 2768 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.970017 5.19442e-05 8304 2 103.7 0.00593814 2768 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.969995 1.57397e-05 8304 2 103.7 0.00176623 2768 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.970005 1.57188e-05 8304 2 103.7 0.0017555 2768 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.969996 1.35047e-05 8304 2 103.7 0.00149649 2768 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.969927 0.000218883 8304 2 103.7 0.025058 2768 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.969994 2.0834e-05 8304 2 103.7 0.00234486 2768 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.969973 8.32328e-05 8304 2 103.7 0.00951196 2768 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.96994 0.000181587 8304 2 103.7 0.0207604 2768 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.970012 3.73019e-05 8304 2 103.7 0.00427704 2768 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97003 9.16483e-05 8304 2 103.7 0.0104321 2768 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.970004 1.17697e-05 8304 2 103.7 0.00130107 2768 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.969965 0.000105332 8304 2 103.7 0.0120207 2768 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.969996 1.30716e-05 8304 2 103.7 0.00142796 2768 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.970006 1.69383e-05 8304 2 103.7 0.00192007 2768 2000000 2000000 135.43134 97619.907 1.2436504 297.53865 43.40944 107.24592 0 0 21276.333 33719.328 -214.64151 -216421.35 -161275.04 5615.89 Loop time of 16101.9 on 32 procs for 2000000 steps with 9101 atoms Performance: 10.732 ns/day, 2.236 hours/ns, 124.209 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 | 8490.7 | 8867.3 | 9198.5 | 164.2 | 55.07 Bond | 2.4057 | 5.9779 | 8.8418 | 63.6 | 0.04 Kspace | 3252.4 | 3580.6 | 3963.4 | 260.2 | 22.24 Neigh | 680.21 | 680.81 | 681.42 | 1.3 | 4.23 Comm | 1021.5 | 1038.4 | 1057.7 | 32.0 | 6.45 Output | 0.012166 | 0.014411 | 0.016578 | 1.1 | 0.00 Modify | 1431.9 | 1641.5 | 1818.5 | 390.5 | 10.19 Other | | 287.3 | | | 1.78 Nlocal: 284.406 ave 298 max 265 min Histogram: 2 0 1 3 4 6 5 4 3 4 Nghost: 7091.09 ave 7185 max 7015 min Histogram: 1 3 7 5 3 2 6 2 1 2 Neighs: 152261 ave 161384 max 141067 min Histogram: 1 2 1 3 7 4 3 8 1 2 Total # of neighbors = 4872364 Ave neighs/atom = 535.36578 Ave special neighs/atom = 1.8929788 Neighbor list builds = 106283 Dangerous builds = 0 undump sci restart 0 dump sci all custom 2000000 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) = 0.257708 grid = 30 30 50 stencil order = 5 estimated absolute RMS force accuracy = 0.0028641952 estimated relative force accuracy = 8.6254386e-06 using double precision KISS FFT 3d grid and FFT values/proc = 6292 1800 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 2 0.970006 1.69383e-05 8304 2 103.7 0.00192007 2768 Per MPI rank memory allocation (min/avg/max) = 12.84 | 13.04 | 13.12 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 167.92545 97619.907 1.2436504 297.53865 43.40944 107.24592 0 0 21276.333 33579.955 -214.64151 -216281.96 -161275.01 5615.89 Loop time of 7.40613e-06 on 32 procs for 0 steps with 9101 atoms 103.0% 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 | | 7.406e-06 | | |100.00 Nlocal: 284.406 ave 298 max 265 min Histogram: 2 0 1 3 4 6 5 4 3 4 Nghost: 7091.09 ave 7185 max 7015 min Histogram: 1 3 7 5 3 2 6 2 1 2 Neighs: 152261 ave 161384 max 141067 min Histogram: 1 2 1 3 7 4 3 8 1 2 Total # of neighbors = 4872364 Ave neighs/atom = 535.36578 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: 4:28:24