#------------------------------------------------------------------------------- # 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 2812 = # of frozen angles find clusters CPU = 0.002 seconds change_box all triclinic Changing box ... triclinic box = (0 0 0) to (36.8271 36.8271 69.281874) 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 (36.8271 36.8271 69.281874) 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 = 0.0151 (../kspace.cpp:325) using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.25615969 grid = 30 30 45 stencil order = 5 estimated absolute RMS force accuracy = 0.0031432339 estimated relative force accuracy = 9.4657554e-06 using double precision KISS FFT 3d grid and FFT values/proc = 5544 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 10 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 0.996059 0.664658 8436 2 97.2022 34.6427 2812 Per MPI rank memory allocation (min/avg/max) = 12.87 | 13 | 13.16 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 7362.5594 93962.523 1.2789064 429.73544 61.834271 215.71841 0 0 21137.571 51382.007 -220.49494 -206540.97 -133743.84 8166.1181 SHAKE stats (type/ave/delta/count) on step 50000 2 0.970007 2.25832e-05 8436 2 103.7 0.00257519 2812 SHAKE stats (type/ave/delta/count) on step 100000 2 0.970013 4.07141e-05 8436 2 103.7 0.00466662 2812 SHAKE stats (type/ave/delta/count) on step 150000 2 0.969998 7.8723e-06 8436 2 103.7 0.000826453 2812 SHAKE stats (type/ave/delta/count) on step 200000 2 0.969977 7.01772e-05 8436 2 103.7 0.00798616 2812 SHAKE stats (type/ave/delta/count) on step 250000 2 0.969962 0.000114902 8436 2 103.7 0.0131538 2812 SHAKE stats (type/ave/delta/count) on step 300000 2 0.969998 8.57706e-06 8436 2 103.7 0.000968688 2812 SHAKE stats (type/ave/delta/count) on step 350000 2 0.970005 1.42868e-05 8436 2 103.7 0.00160276 2812 SHAKE stats (type/ave/delta/count) on step 400000 2 0.970002 7.14878e-06 8436 2 103.7 0.000753099 2812 SHAKE stats (type/ave/delta/count) on step 450000 2 0.969985 4.74173e-05 8436 2 103.7 0.00535954 2812 SHAKE stats (type/ave/delta/count) on step 500000 2 0.969989 3.42012e-05 8436 2 103.7 0.00388827 2812 SHAKE stats (type/ave/delta/count) on step 550000 2 0.970026 7.83828e-05 8436 2 103.7 0.0090028 2812 SHAKE stats (type/ave/delta/count) on step 600000 2 0.970016 4.7185e-05 8436 2 103.7 0.00537468 2812 SHAKE stats (type/ave/delta/count) on step 650000 2 0.969972 8.4619e-05 8436 2 103.7 0.00963626 2812 SHAKE stats (type/ave/delta/count) on step 700000 2 0.969995 1.55088e-05 8436 2 103.7 0.00175412 2812 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97007 0.000209094 8436 2 103.7 0.0239865 2812 SHAKE stats (type/ave/delta/count) on step 800000 2 0.970079 0.000240878 8436 2 103.7 0.027567 2812 SHAKE stats (type/ave/delta/count) on step 850000 2 0.970035 0.000105973 8436 2 103.7 0.0121262 2812 SHAKE stats (type/ave/delta/count) on step 900000 2 0.969989 3.28351e-05 8436 2 103.7 0.00370163 2812 SHAKE stats (type/ave/delta/count) on step 950000 2 0.970011 3.35578e-05 8436 2 103.7 0.00384707 2812 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.970006 1.73277e-05 8436 2 103.7 0.00197926 2812 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.970016 4.66923e-05 8436 2 103.7 0.00538248 2812 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.970001 3.86468e-06 8436 2 103.7 0.000396871 2812 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.969988 3.70172e-05 8436 2 103.7 0.00416715 2812 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.970035 0.000104401 8436 2 103.7 0.011969 2812 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.969988 3.67705e-05 8436 2 103.7 0.00416493 2812 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.969998 8.24312e-06 8436 2 103.7 0.000901796 2812 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.969956 0.000132493 8436 2 103.7 0.0151458 2812 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.96993 0.000210301 8436 2 103.7 0.0240659 2812 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.970008 2.34223e-05 8436 2 103.7 0.00264039 2812 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.970004 1.20438e-05 8436 2 103.7 0.00136976 2812 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.969993 2.11975e-05 8436 2 103.7 0.00238532 2812 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.969996 1.4021e-05 8436 2 103.7 0.00154169 2812 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.970023 6.76171e-05 8436 2 103.7 0.00775996 2812 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.969969 9.43429e-05 8436 2 103.7 0.0107525 2812 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.970009 2.69723e-05 8436 2 103.7 0.00307355 2812 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.970009 2.86512e-05 8436 2 103.7 0.00324118 2812 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.970085 0.0002584 8436 2 103.7 0.0296233 2812 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.970078 0.000233192 8436 2 103.7 0.0267013 2812 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97004 0.000121921 8436 2 103.7 0.0139864 2812 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.970023 7.12259e-05 8436 2 103.7 0.00807198 2812 2000000 2000000 -752.06797 97920.754 1.2272094 296.86139 48.690385 75.379795 0 0 18387.651 47866.882 -211.58191 -207234.55 -140855.95 5641.1573 Loop time of 16802.6 on 32 procs for 2000000 steps with 9188 atoms Performance: 10.284 ns/day, 2.334 hours/ns, 119.029 timesteps/s 99.2% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8683.1 | 9057.6 | 9548.4 | 216.7 | 53.91 Bond | 2.6982 | 5.6216 | 10.67 | 84.8 | 0.03 Kspace | 3523.6 | 4011.7 | 4384.9 | 328.3 | 23.88 Neigh | 730.58 | 731.16 | 731.81 | 1.2 | 4.35 Comm | 1015.6 | 1028.6 | 1039.9 | 19.9 | 6.12 Output | 0.011385 | 0.013682 | 0.01585 | 1.2 | 0.00 Modify | 1500.2 | 1661.7 | 1860 | 374.0 | 9.89 Other | | 306.2 | | | 1.82 Nlocal: 287.125 ave 310 max 269 min Histogram: 4 1 5 6 3 4 3 3 2 1 Nghost: 7185.62 ave 7241 max 7131 min Histogram: 3 0 3 5 5 5 4 3 2 2 Neighs: 154672 ave 167459 max 142833 min Histogram: 2 2 5 6 1 5 5 1 3 2 Total # of neighbors = 4949500 Ave neighs/atom = 538.69177 Ave special neighs/atom = 1.9037875 Neighbor list builds = 106293 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) = 0.25696535 grid = 30 30 48 stencil order = 5 estimated absolute RMS force accuracy = 0.002899315 estimated relative force accuracy = 8.7312009e-06 using double precision KISS FFT 3d grid and FFT values/proc = 5852 1800 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 2 0.970023 7.12259e-05 8436 2 103.7 0.00807198 2812 Per MPI rank memory allocation (min/avg/max) = 12.91 | 13.1 | 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 2000000 2000000 -613.77744 97920.754 1.2272094 296.86139 48.690385 75.379795 0 0 18387.651 48513.654 -211.58191 -207881.4 -140856.03 5641.1573 Loop time of 1.51679e-05 on 32 procs for 0 steps with 9188 atoms 111.5% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 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 | | 1.517e-05 | | |100.00 Nlocal: 287.125 ave 310 max 269 min Histogram: 4 1 5 6 3 4 3 3 2 1 Nghost: 7185.62 ave 7241 max 7131 min Histogram: 3 0 3 5 5 5 4 3 2 2 Neighs: 154672 ave 167459 max 142833 min Histogram: 2 2 5 6 1 5 5 1 3 2 Total # of neighbors = 4949500 Ave neighs/atom = 538.69177 Ave special neighs/atom = 1.9037875 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken log 2.5_NVT.out