#------------------------------------------------------------------------------- # 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 2699 = # of frozen angles find clusters CPU = 0.001 seconds change_box all triclinic Changing box ... triclinic box = (0 0 0) to (45.402 32.1502 62.648044) 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 (45.402 32.1502 62.648044) 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 = 0.024 (../kspace.cpp:325) using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.25869231 grid = 36 27 45 stencil order = 5 estimated absolute RMS force accuracy = 0.0028157339 estimated relative force accuracy = 8.4794989e-06 using double precision KISS FFT 3d grid and FFT values/proc = 5760 1944 generated 0 of 28 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 = 7 5 9 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 0.998963 0.831497 8097 2 96.2435 61.9314 2699 Per MPI rank memory allocation (min/avg/max) = 12.88 | 12.98 | 13.17 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 24882.37 91446.309 1.3291045 427.22241 116.11162 258.26665 0 0 29178.449 38204.441 -226.3957 -218093.7 -150336.43 7943.8987 SHAKE stats (type/ave/delta/count) on step 50000 2 0.969965 0.000104229 8097 2 103.7 0.011887 2699 SHAKE stats (type/ave/delta/count) on step 100000 2 0.969968 9.61563e-05 8097 2 103.7 0.010963 2699 SHAKE stats (type/ave/delta/count) on step 150000 2 0.970018 5.53139e-05 8097 2 103.7 0.00630764 2699 SHAKE stats (type/ave/delta/count) on step 200000 2 0.969944 0.000171545 8097 2 103.7 0.019586 2699 SHAKE stats (type/ave/delta/count) on step 250000 2 0.970016 4.68923e-05 8097 2 103.7 0.00533903 2699 SHAKE stats (type/ave/delta/count) on step 300000 2 0.969937 0.000188848 8097 2 103.7 0.0215828 2699 SHAKE stats (type/ave/delta/count) on step 350000 2 0.96997 9.1848e-05 8097 2 103.7 0.0104635 2699 SHAKE stats (type/ave/delta/count) on step 400000 2 0.969959 0.000123617 8097 2 103.7 0.014141 2699 SHAKE stats (type/ave/delta/count) on step 450000 2 0.970022 6.40442e-05 8097 2 103.7 0.0073687 2699 SHAKE stats (type/ave/delta/count) on step 500000 2 0.970023 6.8122e-05 8097 2 103.7 0.00777873 2699 SHAKE stats (type/ave/delta/count) on step 550000 2 0.969973 8.17563e-05 8097 2 103.7 0.00931197 2699 SHAKE stats (type/ave/delta/count) on step 600000 2 0.969958 0.000126211 8097 2 103.7 0.0144494 2699 SHAKE stats (type/ave/delta/count) on step 650000 2 0.969964 0.000110939 8097 2 103.7 0.0126485 2699 SHAKE stats (type/ave/delta/count) on step 700000 2 0.969984 4.81877e-05 8097 2 103.7 0.00549372 2699 SHAKE stats (type/ave/delta/count) on step 750000 2 0.969972 8.45235e-05 8097 2 103.7 0.00967296 2699 SHAKE stats (type/ave/delta/count) on step 800000 2 0.970054 0.000162825 8097 2 103.7 0.018651 2699 SHAKE stats (type/ave/delta/count) on step 850000 2 0.969996 1.29368e-05 8097 2 103.7 0.00140544 2699 SHAKE stats (type/ave/delta/count) on step 900000 2 0.969963 0.000114381 8097 2 103.7 0.0129888 2699 SHAKE stats (type/ave/delta/count) on step 950000 2 0.970014 4.42276e-05 8097 2 103.7 0.00495013 2699 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.970053 0.000160169 8097 2 103.7 0.0183697 2699 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.970036 0.000108844 8097 2 103.7 0.0124315 2699 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.969958 0.00012751 8097 2 103.7 0.0145482 2699 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.969982 5.63221e-05 8097 2 103.7 0.00642203 2699 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.970015 4.43671e-05 8097 2 103.7 0.00506098 2699 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.970028 8.349e-05 8097 2 103.7 0.00962208 2699 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.970038 0.000116335 8097 2 103.7 0.0132552 2699 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.970002 7.43334e-06 8097 2 103.7 0.000846229 2699 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97003 9.02795e-05 8097 2 103.7 0.0103242 2699 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.969964 0.000111961 8097 2 103.7 0.0127576 2699 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.969995 1.77343e-05 8097 2 103.7 0.00199745 2699 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.970006 1.78865e-05 8097 2 103.7 0.00202952 2699 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.969956 0.000131413 8097 2 103.7 0.0149878 2699 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.969946 0.000161408 8097 2 103.7 0.0184204 2699 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.969999 3.92023e-06 8097 2 103.7 0.000406074 2699 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.970025 7.43995e-05 8097 2 103.7 0.00854666 2699 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.969923 0.000235413 8097 2 103.7 0.0269815 2699 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.970018 5.37072e-05 8097 2 103.7 0.00613592 2699 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.970033 9.92878e-05 8097 2 103.7 0.0113793 2699 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.969945 0.000168587 8097 2 103.7 0.0192544 2699 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.969995 1.61687e-05 8097 2 103.7 0.00180063 2699 2000000 2000000 -33.32683 96454.14 1.2600984 299.16044 41.257457 65.543315 0 0 22949.527 21200.54 -214.6414 -220301.99 -176045.13 5562.677 Loop time of 15921 on 32 procs for 2000000 steps with 8938 atoms Performance: 10.854 ns/day, 2.211 hours/ns, 125.620 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 | 7927.6 | 8690.6 | 9126.3 | 266.0 | 54.59 Bond | 2.2517 | 5.2052 | 9.9022 | 86.6 | 0.03 Kspace | 3179.8 | 3616.9 | 4378.8 | 413.9 | 22.72 Neigh | 719.94 | 721.16 | 722.06 | 2.3 | 4.53 Comm | 942.34 | 956.37 | 968.2 | 27.1 | 6.01 Output | 0.010817 | 0.013068 | 0.015169 | 1.2 | 0.00 Modify | 1439.2 | 1613.9 | 1835.8 | 411.8 | 10.14 Other | | 316.8 | | | 1.99 Nlocal: 279.312 ave 305 max 261 min Histogram: 3 2 6 5 4 4 4 3 0 1 Nghost: 6868.25 ave 6958 max 6778 min Histogram: 3 1 1 3 8 7 3 2 2 2 Neighs: 148682 ave 163938 max 134984 min Histogram: 1 1 8 2 5 6 4 2 2 1 Total # of neighbors = 4757831 Ave neighs/atom = 532.31495 Ave special neighs/atom = 1.8722309 Neighbor list builds = 105009 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) = 0.25743922 grid = 36 27 45 stencil order = 5 estimated absolute RMS force accuracy = 0.0030112685 estimated relative force accuracy = 9.0683458e-06 using double precision KISS FFT 3d grid and FFT values/proc = 5760 1944 generated 0 of 28 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 2 0.969995 1.61687e-05 8097 2 103.7 0.00180063 2699 Per MPI rank memory allocation (min/avg/max) = 12.89 | 13.05 | 13.18 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 -61.910943 96454.14 1.2600984 299.16044 41.257457 65.543315 0 0 22949.527 20142.578 -214.6414 -219244.03 -176045.12 5562.677 Loop time of 1.35072e-05 on 32 procs for 0 steps with 8938 atoms 113.4% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 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 | | 1.351e-05 | | |100.00 Nlocal: 279.312 ave 305 max 261 min Histogram: 3 2 6 5 4 4 4 3 0 1 Nghost: 6868.25 ave 6958 max 6778 min Histogram: 3 1 1 3 8 7 3 2 2 2 Neighs: 148682 ave 163938 max 134984 min Histogram: 1 1 8 2 5 6 4 2 2 1 Total # of neighbors = 4757831 Ave neighs/atom = 532.31495 Ave special neighs/atom = 1.8722309 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken Total wall time: 4:25:22