#------------------------------------------------------------------------------- # Stage 2.5: NPT integration for 2 ns with a timestep of 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 2699 = # of frozen angles find clusters CPU = 0.001 seconds change_box all triclinic Changing box ... WARNING: Triclinic box skew is large (../domain.cpp:219) triclinic box = (0 0 0) to (28.02072 45.401823 69.1) with tilt (18.680117 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 ... WARNING: Triclinic box skew is large (../domain.cpp:219) triclinic box = (0 0 0) to (28.02072 45.401823 69.1) with tilt (18.680117 0 0) fix 1 movable npt temp 298.2 298.2 100 z 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 2.5_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 2.5_instantaneous.txt restart 2000000 2.5.restart dump sci all custom 200000 2.5.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) = 0.25726526 grid = 24 50 48 stencil order = 5 estimated absolute RMS force accuracy = 0.003196358 estimated relative force accuracy = 9.6257371e-06 using double precision KISS FFT 3d grid and FFT values/proc = 7220 2400 generated 0 of 28 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.97 9.87876e-13 8097 2 103.7 8.90026e-11 2699 Per MPI rank memory allocation (min/avg/max) = 13.06 | 13.3 | 13.75 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 6165.4313 87908.451 1.3825941 297.68356 36.042263 62.943163 0 0 25155.175 17426.279 -235.50695 -219124.39 -176443.95 5535.2153 SHAKE stats (type/ave/delta/count) on step 50000 2 0.969994 1.89679e-05 8097 2 103.7 0.00213311 2699 SHAKE stats (type/ave/delta/count) on step 100000 2 0.969931 0.000208671 8097 2 103.7 0.0238539 2699 SHAKE stats (type/ave/delta/count) on step 150000 2 0.969986 4.47849e-05 8097 2 103.7 0.00510371 2699 SHAKE stats (type/ave/delta/count) on step 200000 2 0.969969 9.36519e-05 8097 2 103.7 0.0106938 2699 SHAKE stats (type/ave/delta/count) on step 250000 2 0.970054 0.000164935 8097 2 103.7 0.0188957 2699 SHAKE stats (type/ave/delta/count) on step 300000 2 0.970007 2.10591e-05 8097 2 103.7 0.00241632 2699 SHAKE stats (type/ave/delta/count) on step 350000 2 0.970003 8.57371e-06 8097 2 103.7 0.000955299 2699 SHAKE stats (type/ave/delta/count) on step 400000 2 0.969998 7.19586e-06 8097 2 103.7 0.000783942 2699 SHAKE stats (type/ave/delta/count) on step 450000 2 0.969992 2.46536e-05 8097 2 103.7 0.00279308 2699 SHAKE stats (type/ave/delta/count) on step 500000 2 0.970019 5.78714e-05 8097 2 103.7 0.0066314 2699 SHAKE stats (type/ave/delta/count) on step 550000 2 0.970018 5.27891e-05 8097 2 103.7 0.0060105 2699 SHAKE stats (type/ave/delta/count) on step 600000 2 0.969999 5.59851e-06 8097 2 103.7 0.000611418 2699 SHAKE stats (type/ave/delta/count) on step 650000 2 0.970054 0.00016064 8097 2 103.7 0.0184115 2699 SHAKE stats (type/ave/delta/count) on step 700000 2 0.970018 5.4112e-05 8097 2 103.7 0.00619064 2699 SHAKE stats (type/ave/delta/count) on step 750000 2 0.969976 7.41615e-05 8097 2 103.7 0.00847092 2699 SHAKE stats (type/ave/delta/count) on step 800000 2 0.969976 7.3442e-05 8097 2 103.7 0.00834317 2699 SHAKE stats (type/ave/delta/count) on step 850000 2 0.969965 0.000107498 8097 2 103.7 0.0122964 2699 SHAKE stats (type/ave/delta/count) on step 900000 2 0.970019 5.73318e-05 8097 2 103.7 0.00655028 2699 SHAKE stats (type/ave/delta/count) on step 950000 2 0.969971 8.96668e-05 8097 2 103.7 0.0102546 2699 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.969955 0.000135654 8097 2 103.7 0.0154997 2699 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.969991 2.91637e-05 8097 2 103.7 0.00331049 2699 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.969983 5.17572e-05 8097 2 103.7 0.00588568 2699 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.969937 0.000192176 8097 2 103.7 0.0219093 2699 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.969962 0.000115562 8097 2 103.7 0.0131907 2699 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.969947 0.000157208 8097 2 103.7 0.0179477 2699 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.970019 5.58762e-05 8097 2 103.7 0.00636842 2699 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.970002 8.03812e-06 8097 2 103.7 0.000869499 2699 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.970018 5.54622e-05 8097 2 103.7 0.00630809 2699 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.970041 0.00012075 8097 2 103.7 0.0138303 2699 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.970019 5.68129e-05 8097 2 103.7 0.006428 2699 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.969996 1.16913e-05 8097 2 103.7 0.00129442 2699 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97002 6.05822e-05 8097 2 103.7 0.00692403 2699 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.969972 8.50014e-05 8097 2 103.7 0.00969463 2699 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.970019 5.78462e-05 8097 2 103.7 0.00659459 2699 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.969999 4.00483e-06 8097 2 103.7 0.000416352 2699 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.969995 1.73371e-05 8097 2 103.7 0.00191272 2699 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.969979 6.52405e-05 8097 2 103.7 0.00743267 2699 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.969912 0.000263604 8097 2 103.7 0.0301621 2699 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.969975 7.71682e-05 8097 2 103.7 0.00879199 2699 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.969976 7.3583e-05 8097 2 103.7 0.00836835 2699 2000000 2000000 24.914414 96518.885 1.2592531 295.22587 45.194814 63.12517 0 0 22808.984 20326.031 -214.49741 -219097.79 -175854.45 5489.5163 Loop time of 17078.2 on 32 procs for 2000000 steps with 8938 atoms Performance: 10.118 ns/day, 2.372 hours/ns, 117.108 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 | 8181.9 | 8728.2 | 9314 | 289.6 | 51.11 Bond | 2.3897 | 5.381 | 10.704 | 98.7 | 0.03 Kspace | 3748.1 | 4337.2 | 4883.7 | 413.6 | 25.40 Neigh | 729.16 | 729.71 | 730.31 | 1.2 | 4.27 Comm | 1080.2 | 1100 | 1120.6 | 35.1 | 6.44 Output | 0.0091711 | 0.011464 | 0.013572 | 1.2 | 0.00 Modify | 1589 | 1857.5 | 2093.2 | 492.0 | 10.88 Other | | 320.3 | | | 1.88 Nlocal: 279.312 ave 298 max 258 min Histogram: 1 2 3 5 5 2 3 6 2 3 Nghost: 7005.44 ave 7111 max 6904 min Histogram: 3 1 3 6 1 6 7 2 2 1 Neighs: 148569 ave 163062 max 136065 min Histogram: 3 4 3 3 5 3 5 3 2 1 Total # of neighbors = 4754199 Ave neighs/atom = 531.90859 Ave special neighs/atom = 1.8722309 Neighbor list builds = 105989 Dangerous builds = 0 undump sci restart 0 dump sci all custom 2000000 2.5.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) = 0.25829155 grid = 24 45 50 stencil order = 5 estimated absolute RMS force accuracy = 0.0028238997 estimated relative force accuracy = 8.5040901e-06 using double precision KISS FFT 3d grid and FFT values/proc = 6498 2160 generated 0 of 28 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 2 0.969976 7.3583e-05 8097 2 103.7 0.00836835 2699 Per MPI rank memory allocation (min/avg/max) = 13.13 | 13.4 | 13.74 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 -114.34534 96518.885 1.2592531 295.22587 45.194814 63.12517 0 0 22808.984 21192.653 -214.49741 -219964.33 -175854.37 5489.5163 Loop time of 8.35541e-06 on 32 procs for 0 steps with 8938 atoms 109.6% 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 | | 8.355e-06 | | |100.00 Nlocal: 279.312 ave 298 max 258 min Histogram: 1 2 3 5 5 2 3 6 2 3 Nghost: 7005.44 ave 7111 max 6904 min Histogram: 3 1 3 6 1 6 7 2 2 1 Neighs: 148569 ave 163062 max 136065 min Histogram: 3 4 3 3 5 3 5 3 2 1 Total # of neighbors = 4754199 Ave neighs/atom = 531.90859 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: 9:34:53