#------------------------------------------------------------------------------- # Stage 2.4: NPT integration for 3 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 2297 = # of frozen angles find clusters CPU = 0.001 seconds change_box all triclinic Changing box ... triclinic box = (0 0 0) to (29.25318 24.458 118.4) 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 (29.25318 24.458 118.4) with tilt (0 0 0) fix 1 movable npt temp 298.2 298.2 100 z 1 1 100 drag 0 mtk yes nreset 60000 fix 2 movable ave/time 1 299999 300000 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 300 1 300 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 3000000 2.4.restart dump sci all custom 300000 2.4.xyz id mol type q xs ys zs timestep 1 run 3000000 PPPM initialization ... WARNING: System is not charge neutral, net charge = 0.0204 (../kspace.cpp:325) using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.25920223 grid = 25 24 72 stencil order = 5 estimated absolute RMS force accuracy = 0.0027365003 estimated relative force accuracy = 8.2408893e-06 using double precision KISS FFT 3d grid and FFT values/proc = 5776 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 = 5 4 17 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 1.00217 0.499931 6891 2 97.6814 16.5944 2297 Per MPI rank memory allocation (min/avg/max) = 12.55 | 12.9 | 13.09 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 -1438.9226 84712.154 1.2725888 422.44549 22.599562 98.279561 0 0 21649.497 7573.583 -194.61338 -200669.12 -171325.16 6942.1337 SHAKE stats (type/ave/delta/count) on step 50000 2 0.970068 0.000204106 6891 2 103.7 0.0234157 2297 SHAKE stats (type/ave/delta/count) on step 100000 2 0.969999 5.57016e-06 6891 2 103.7 0.000624043 2297 SHAKE stats (type/ave/delta/count) on step 150000 2 0.969983 5.19864e-05 6891 2 103.7 0.00592132 2297 SHAKE stats (type/ave/delta/count) on step 200000 2 0.970024 7.08447e-05 6891 2 103.7 0.00812528 2297 SHAKE stats (type/ave/delta/count) on step 250000 2 0.969993 2.30633e-05 6891 2 103.7 0.00258173 2297 SHAKE stats (type/ave/delta/count) on step 300000 2 0.970027 8.18847e-05 6891 2 103.7 0.00933504 2297 SHAKE stats (type/ave/delta/count) on step 350000 2 0.970021 6.1129e-05 6891 2 103.7 0.00694252 2297 SHAKE stats (type/ave/delta/count) on step 400000 2 0.969972 8.31369e-05 6891 2 103.7 0.00946496 2297 SHAKE stats (type/ave/delta/count) on step 450000 2 0.970009 2.83348e-05 6891 2 103.7 0.0031958 2297 SHAKE stats (type/ave/delta/count) on step 500000 2 0.969982 5.55717e-05 6891 2 103.7 0.00627797 2297 SHAKE stats (type/ave/delta/count) on step 550000 2 0.969954 0.000136167 6891 2 103.7 0.0155487 2297 SHAKE stats (type/ave/delta/count) on step 600000 2 0.970019 5.81449e-05 6891 2 103.7 0.00661671 2297 SHAKE stats (type/ave/delta/count) on step 650000 2 0.969936 0.000191111 6891 2 103.7 0.02182 2297 SHAKE stats (type/ave/delta/count) on step 700000 2 0.969965 0.000105824 6891 2 103.7 0.0120358 2297 SHAKE stats (type/ave/delta/count) on step 750000 2 0.969934 0.000196815 6891 2 103.7 0.022492 2297 SHAKE stats (type/ave/delta/count) on step 800000 2 0.970043 0.000128177 6891 2 103.7 0.0146919 2297 SHAKE stats (type/ave/delta/count) on step 850000 2 0.970012 3.6082e-05 6891 2 103.7 0.00413206 2297 SHAKE stats (type/ave/delta/count) on step 900000 2 0.970048 0.000142501 6891 2 103.7 0.0163237 2297 SHAKE stats (type/ave/delta/count) on step 950000 2 0.969987 3.94476e-05 6891 2 103.7 0.00441984 2297 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.9701 0.000296594 6891 2 103.7 0.0340465 2297 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.969963 0.000110107 6891 2 103.7 0.0125453 2297 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97001 3.0359e-05 6891 2 103.7 0.00342606 2297 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.969987 3.86544e-05 6891 2 103.7 0.00438388 2297 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.969984 4.67101e-05 6891 2 103.7 0.00525892 2297 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.969977 6.92149e-05 6891 2 103.7 0.00781998 2297 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.970069 0.000203418 6891 2 103.7 0.0233165 2297 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.969985 4.50231e-05 6891 2 103.7 0.00511488 2297 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.969992 2.58853e-05 6891 2 103.7 0.0029103 2297 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.969988 3.51148e-05 6891 2 103.7 0.00398832 2297 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.969984 4.83121e-05 6891 2 103.7 0.00543992 2297 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.969994 1.82776e-05 6891 2 103.7 0.00205679 2297 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.969983 4.9286e-05 6891 2 103.7 0.00562136 2297 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.969957 0.000127582 6891 2 103.7 0.0145263 2297 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.969993 2.07926e-05 6891 2 103.7 0.00236394 2297 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.970031 9.35941e-05 6891 2 103.7 0.0106709 2297 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.96998 6.046e-05 6891 2 103.7 0.0068728 2297 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.970015 4.39979e-05 6891 2 103.7 0.00504009 2297 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.969957 0.000127978 6891 2 103.7 0.0146158 2297 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.970055 0.000163061 6891 2 103.7 0.0187007 2297 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.970047 0.000139163 6891 2 103.7 0.015914 2297 SHAKE stats (type/ave/delta/count) on step 2050000 2 0.970042 0.000126048 6891 2 103.7 0.0144098 2297 SHAKE stats (type/ave/delta/count) on step 2100000 2 0.969971 8.5787e-05 6891 2 103.7 0.00974709 2297 SHAKE stats (type/ave/delta/count) on step 2150000 2 0.969996 1.20054e-05 6891 2 103.7 0.00133015 2297 SHAKE stats (type/ave/delta/count) on step 2200000 2 0.970007 2.24388e-05 6891 2 103.7 0.00253176 2297 SHAKE stats (type/ave/delta/count) on step 2250000 2 0.96999 3.26141e-05 6891 2 103.7 0.00366907 2297 SHAKE stats (type/ave/delta/count) on step 2300000 2 0.969948 0.000157136 6891 2 103.7 0.0179344 2297 SHAKE stats (type/ave/delta/count) on step 2350000 2 0.969966 0.00010223 6891 2 103.7 0.0116305 2297 SHAKE stats (type/ave/delta/count) on step 2400000 2 0.970038 0.000114638 6891 2 103.7 0.0131918 2297 SHAKE stats (type/ave/delta/count) on step 2450000 2 0.969986 4.20333e-05 6891 2 103.7 0.00476997 2297 SHAKE stats (type/ave/delta/count) on step 2500000 2 0.970062 0.000186778 6891 2 103.7 0.021426 2297 SHAKE stats (type/ave/delta/count) on step 2550000 2 0.97004 0.000121271 6891 2 103.7 0.0138756 2297 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.969983 5.07464e-05 6891 2 103.7 0.00577932 2297 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.969983 5.06828e-05 6891 2 103.7 0.00576551 2297 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.969994 1.93542e-05 6891 2 103.7 0.0021505 2297 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.969994 2.04483e-05 6891 2 103.7 0.0022618 2297 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.969992 2.45252e-05 6891 2 103.7 0.00275774 2297 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.96999 3.23481e-05 6891 2 103.7 0.00368106 2297 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.970034 0.000100801 6891 2 103.7 0.0115795 2297 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.969943 0.000170389 6891 2 103.7 0.0194517 2297 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.969972 8.34261e-05 6891 2 103.7 0.00952147 2297 3000000 3000000 -233.42826 80971.351 1.3313813 294.64235 123.13061 148.85575 0 0 19715.758 20190.9 -203.60435 -200601.26 -160422.61 4841.9183 Loop time of 25121.4 on 32 procs for 3000000 steps with 7811 atoms Performance: 10.318 ns/day, 2.326 hours/ns, 119.420 timesteps/s 99.0% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 10878 | 11903 | 15625 |1294.9 | 47.38 Bond | 3.9479 | 12.008 | 37.397 | 276.6 | 0.05 Kspace | 4125 | 7877.6 | 8915.2 |1609.4 | 31.36 Neigh | 1190.6 | 1194.9 | 1199.3 | 6.7 | 4.76 Comm | 1330.9 | 1394 | 1486.1 | 129.8 | 5.55 Output | 0.013307 | 0.015346 | 0.017307 | 1.0 | 0.00 Modify | 2189.7 | 2376.4 | 2648 | 303.0 | 9.46 Other | | 363.3 | | | 1.45 Nlocal: 244.094 ave 302 max 220 min Histogram: 4 10 7 5 2 0 2 0 1 1 Nghost: 6717 ave 7219 max 6398 min Histogram: 12 4 1 3 0 1 2 2 4 3 Neighs: 135738 ave 192053 max 116847 min Histogram: 9 9 7 3 0 0 0 2 1 1 Total # of neighbors = 4343632 Ave neighs/atom = 556.09167 Ave special neighs/atom = 1.9743951 Neighbor list builds = 161546 Dangerous builds = 0 undump sci restart 0 dump sci all custom 3000000 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) = 0.26028481 grid = 25 24 72 stencil order = 5 estimated absolute RMS force accuracy = 0.0025861148 estimated relative force accuracy = 7.788008e-06 using double precision KISS FFT 3d grid and FFT values/proc = 5776 1800 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 3000000 2 0.969972 8.34261e-05 6891 2 103.7 0.00952147 2297 Per MPI rank memory allocation (min/avg/max) = 12.87 | 12.98 | 13.48 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 3000000 3000000 -394.48457 80971.351 1.3313813 294.64235 123.13061 148.85575 0 0 19715.758 21021.951 -203.60435 -201432.3 -160422.61 4841.9183 Loop time of 1.59179e-05 on 32 procs for 0 steps with 7811 atoms 107.8% 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 | | 1.592e-05 | | |100.00 Nlocal: 244.094 ave 302 max 220 min Histogram: 4 10 7 5 2 0 2 0 1 1 Nghost: 6717 ave 7219 max 6398 min Histogram: 12 4 1 3 0 1 2 2 4 3 Neighs: 135738 ave 192053 max 116847 min Histogram: 9 9 7 3 0 0 0 2 1 1 Total # of neighbors = 4343632 Ave neighs/atom = 556.09167 Ave special neighs/atom = 1.9743951 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken log 2.5_NVT.out