#------------------------------------------------------------------------------- # Stage 2.4: 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 360 = # 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 21) 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 21) with tilt (0 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 2.4_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 = 0.006 (../kspace.cpp:325) using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.26708433 grid = 24 24 20 stencil order = 5 estimated absolute RMS force accuracy = 0.0020069314 estimated relative force accuracy = 6.0438145e-06 using double precision KISS FFT 3d grid and FFT values/proc = 2873 360 generated 0 of 10 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 3 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 1.01645 0.109231 1080 2 96.7541 9.40626 360 Per MPI rank memory allocation (min/avg/max) = 11.89 | 11.95 | 12.09 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 4667.0736 15024.96 1.5149382 397.69212 19.052363 86.448592 0 0 5705.9038 -5336.8189 -48.594294 -49739.663 -49265.077 1279.0948 SHAKE stats (type/ave/delta/count) on step 50000 2 0.969926 0.000225897 1080 2 103.699 0.0256021 360 SHAKE stats (type/ave/delta/count) on step 100000 2 0.969983 5.0248e-05 1080 2 103.7 0.00567675 360 SHAKE stats (type/ave/delta/count) on step 150000 2 0.970084 0.00024707 1080 2 103.701 0.0280202 360 SHAKE stats (type/ave/delta/count) on step 200000 2 0.969933 0.000197462 1080 2 103.7 0.0225399 360 SHAKE stats (type/ave/delta/count) on step 250000 2 0.969994 1.87433e-05 1080 2 103.7 0.00214218 360 SHAKE stats (type/ave/delta/count) on step 300000 2 0.970044 0.000130866 1080 2 103.7 0.0150075 360 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97001 2.80441e-05 1080 2 103.7 0.00322637 360 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97003 8.93881e-05 1080 2 103.7 0.0101811 360 SHAKE stats (type/ave/delta/count) on step 450000 2 0.969931 0.00020963 1080 2 103.699 0.0238261 360 SHAKE stats (type/ave/delta/count) on step 500000 2 0.96997 9.10833e-05 1080 2 103.7 0.0103151 360 SHAKE stats (type/ave/delta/count) on step 550000 2 0.970013 3.99706e-05 1080 2 103.7 0.00455412 360 SHAKE stats (type/ave/delta/count) on step 600000 2 0.970093 0.000279937 1080 2 103.701 0.0320299 360 SHAKE stats (type/ave/delta/count) on step 650000 2 0.970109 0.000328123 1080 2 103.701 0.037585 360 SHAKE stats (type/ave/delta/count) on step 700000 2 0.969909 0.000275936 1080 2 103.699 0.0315362 360 SHAKE stats (type/ave/delta/count) on step 750000 2 0.969941 0.000179167 1080 2 103.7 0.020043 360 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 2.50614e-06 1080 2 103.7 0.000214282 360 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97004 0.000119791 1080 2 103.7 0.0134832 360 SHAKE stats (type/ave/delta/count) on step 900000 2 0.970006 1.88824e-05 1080 2 103.7 0.00215249 360 SHAKE stats (type/ave/delta/count) on step 950000 2 0.970032 9.61354e-05 1080 2 103.7 0.0109394 360 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.970107 0.000317256 1080 2 103.701 0.0364478 360 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.970201 0.000598967 1080 2 103.702 0.0674875 360 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.969906 0.000273173 1080 2 103.699 0.0312967 360 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.970006 1.8532e-05 1080 2 103.7 0.00209784 360 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.969922 0.000233141 1080 2 103.699 0.0266451 360 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.969962 0.000112395 1080 2 103.7 0.0128379 360 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.969986 4.34977e-05 1080 2 103.7 0.00485996 360 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.969918 0.000240823 1080 2 103.699 0.0275126 360 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.969862 0.000406815 1080 2 103.699 0.0465445 360 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.969948 0.000153311 1080 2 103.7 0.0174464 360 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.970014 4.03523e-05 1080 2 103.7 0.00456303 360 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.970047 0.000140314 1080 2 103.7 0.0159606 360 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.969871 0.000383104 1080 2 103.699 0.0432362 360 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.970032 9.60239e-05 1080 2 103.7 0.0110121 360 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.969995 1.68248e-05 1080 2 103.7 0.00191302 360 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.970151 0.000462863 1080 2 103.701 0.0515725 360 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.970036 0.00010803 1080 2 103.7 0.0122727 360 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.970065 0.000196287 1080 2 103.7 0.022474 360 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.970027 8.02141e-05 1080 2 103.7 0.00931304 360 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.970104 0.000315504 1080 2 103.701 0.0357645 360 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.970009 2.60772e-05 1080 2 103.7 0.00289333 360 2000000 2000000 -1428.1794 13106.344 1.7367074 297.24153 73.74685 125.17347 0 0 4699.3714 -2224.3625 -55.707929 -49737.488 -47063.558 956.01616 Loop time of 4270.47 on 32 procs for 2000000 steps with 1440 atoms Performance: 40.464 ns/day, 0.593 hours/ns, 468.332 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 | 1596.4 | 1800 | 2016.8 | 196.0 | 42.15 Bond | 4.2421 | 5.8749 | 7.297 | 32.9 | 0.14 Kspace | 805.08 | 1026.1 | 1230.7 | 263.7 | 24.03 Neigh | 102.18 | 102.52 | 103.15 | 2.2 | 2.40 Comm | 558.33 | 568.97 | 578.86 | 22.1 | 13.32 Output | 0.0061244 | 0.0070043 | 0.007751 | 0.6 | 0.00 Modify | 726.62 | 733.13 | 738.7 | 9.9 | 17.17 Other | | 33.86 | | | 0.79 Nlocal: 45 ave 51 max 36 min Histogram: 2 1 1 1 2 3 11 4 5 2 Nghost: 4838.47 ave 4878 max 4785 min Histogram: 2 0 1 4 10 1 2 3 5 4 Neighs: 28377.8 ave 32419 max 22608 min Histogram: 2 1 2 1 1 6 9 6 3 1 Total # of neighbors = 908088 Ave neighs/atom = 630.61667 Ave special neighs/atom = 2.3333333 Neighbor list builds = 73176 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) = 0.26769016 grid = 24 24 18 stencil order = 5 estimated absolute RMS force accuracy = 0.0020509213 estimated relative force accuracy = 6.1762887e-06 using double precision KISS FFT 3d grid and FFT values/proc = 2704 360 generated 0 of 10 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 2 0.970009 2.60772e-05 1080 2 103.7 0.00289333 360 Per MPI rank memory allocation (min/avg/max) = 11.89 | 12.03 | 12.09 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 2000000 2000000 -1378.4896 13106.344 1.7367074 297.24153 73.74685 125.17347 0 0 4699.3714 -2112.4551 -55.707929 -49849.395 -47063.559 956.01616 Loop time of 1.54382e-05 on 32 procs for 0 steps with 1440 atoms 108.3% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 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 | | 1.544e-05 | | |100.00 Nlocal: 45 ave 51 max 36 min Histogram: 2 1 1 1 2 3 11 4 5 2 Nghost: 4838.47 ave 4878 max 4785 min Histogram: 2 0 1 4 10 1 2 3 5 4 Neighs: 28377.8 ave 32419 max 22608 min Histogram: 2 1 2 1 1 6 9 6 3 1 Total # of neighbors = 908088 Ave neighs/atom = 630.61667 Ave special neighs/atom = 2.3333333 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken Total wall time: 1:11:12