#------------------------------------------------------------------------------- # 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 2768 = # of frozen angles find clusters CPU = 0.002 seconds change_box all triclinic Changing box ... triclinic box = (0 0 0) to (35.89352 35.89352 72.07658) 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 (35.89352 35.89352 72.07658) 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 = 0.0206 (../kspace.cpp:325) using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.25787546 grid = 30 30 48 stencil order = 5 estimated absolute RMS force accuracy = 0.002900781 estimated relative force accuracy = 8.7356158e-06 using double precision KISS FFT 3d grid and FFT values/proc = 9196 2700 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 11 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 0.996547 0.69591 8304 2 97.542 28.0098 2768 Per MPI rank memory allocation (min/avg/max) = 13.73 | 14.15 | 14.31 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 10613.416 92859.485 1.3074059 428.55654 87.588636 219.17828 0 0 24345.085 36916.542 -225.64506 -215763.24 -154194.84 8088.7858 SHAKE stats (type/ave/delta/count) on step 50000 2 0.969989 3.51517e-05 8304 2 103.7 0.00396884 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.969942 0.000173475 8304 2 103.7 0.0198327 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.969914 0.000259351 8304 2 103.7 0.0296381 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.969997 1.06185e-05 8304 2 103.7 0.00116158 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.970011 3.17827e-05 8304 2 103.7 0.00361643 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.970053 0.000157722 8304 2 103.7 0.0180532 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.970001 4.44654e-06 8304 2 103.7 0.000487198 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97001 2.98047e-05 8304 2 103.7 0.00334547 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.969908 0.000278179 8304 2 103.7 0.0318374 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.970009 2.7985e-05 8304 2 103.7 0.00314406 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97004 0.000121655 8304 2 103.7 0.0139159 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.969977 6.9956e-05 8304 2 103.7 0.00794672 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.970002 7.37071e-06 8304 2 103.7 0.000840624 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.970006 1.91243e-05 8304 2 103.7 0.002193 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.969976 7.14214e-05 8304 2 103.7 0.00810229 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.969955 0.000136377 8304 2 103.7 0.0156274 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.969978 6.87869e-05 8304 2 103.7 0.00783487 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.969932 0.000205258 8304 2 103.7 0.0234868 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.970032 9.54829e-05 8304 2 103.7 0.0109641 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.969973 8.35319e-05 8304 2 103.7 0.00942928 2768 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.970027 8.19646e-05 8304 2 103.7 0.00933726 2768 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.970031 9.3562e-05 8304 2 103.7 0.0107084 2768 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.969928 0.000213228 8304 2 103.7 0.0244273 2768 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.969929 0.000215096 8304 2 103.7 0.0245984 2768 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.96999 3.07898e-05 8304 2 103.7 0.00345753 2768 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.969983 5.30594e-05 8304 2 103.7 0.00602774 2768 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.969962 0.000114916 8304 2 103.7 0.0130735 2768 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.969975 7.70513e-05 8304 2 103.7 0.00875501 2768 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.970044 0.000132551 8304 2 103.7 0.0151812 2768 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.969973 8.26265e-05 8304 2 103.7 0.009424 2768 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.969962 0.000115385 8304 2 103.7 0.0131641 2768 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97001 3.1772e-05 8304 2 103.7 0.00357245 2768 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.970001 4.78327e-06 8304 2 103.7 0.000514888 2768 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97002 6.06693e-05 8304 2 103.7 0.00696335 2768 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.969959 0.00012286 8304 2 103.7 0.0140482 2768 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.970014 4.25908e-05 8304 2 103.7 0.00486688 2768 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.969966 0.000102444 8304 2 103.7 0.0116857 2768 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97001 2.90967e-05 8304 2 103.7 0.00332584 2768 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.969988 3.82012e-05 8304 2 103.7 0.00431221 2768 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.970011 3.38398e-05 8304 2 103.7 0.00385945 2768 2000000 2000000 -681.04183 98081.663 1.2377954 300.68015 37.707015 70.103397 0 0 21028.135 34016.585 -213.63101 -216393.09 -161240.55 5675.1842 Loop time of 26878.3 on 16 procs for 2000000 steps with 9101 atoms Performance: 6.429 ns/day, 3.733 hours/ns, 74.409 timesteps/s 98.9% CPU use with 16 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 17152 | 17702 | 18437 | 315.2 | 65.86 Bond | 4.1947 | 9.0928 | 14.769 | 75.8 | 0.03 Kspace | 4211.7 | 4951 | 5503.6 | 598.1 | 18.42 Neigh | 1416.2 | 1416.6 | 1416.9 | 0.6 | 5.27 Comm | 665.08 | 675.2 | 685.88 | 25.1 | 2.51 Output | 0.015149 | 0.016924 | 0.018507 | 0.8 | 0.00 Modify | 1935.9 | 1972.9 | 2006.3 | 38.2 | 7.34 Other | | 152 | | | 0.57 Nlocal: 568.812 ave 603 max 548 min Histogram: 3 1 3 2 3 0 3 0 0 1 Nghost: 8650.12 ave 8737 max 8584 min Histogram: 3 1 1 1 3 3 2 1 0 1 Neighs: 303234 ave 328881 max 289458 min Histogram: 2 3 1 5 1 3 0 0 0 1 Total # of neighbors = 4851743 Ave neighs/atom = 533.09999 Ave special neighs/atom = 1.8929788 Neighbor list builds = 106230 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) = 0.25757539 grid = 30 30 50 stencil order = 5 estimated absolute RMS force accuracy = 0.0028859317 estimated relative force accuracy = 8.6908976e-06 using double precision KISS FFT 3d grid and FFT values/proc = 9196 3600 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 2 0.970011 3.38398e-05 8304 2 103.7 0.00385945 2768 Per MPI rank memory allocation (min/avg/max) = 14.13 | 14.29 | 14.41 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 -616.39379 98081.663 1.2377954 300.68015 37.707015 70.103397 0 0 21028.135 33766.9 -213.63101 -216143.29 -161240.45 5675.1842 Loop time of 4.28463e-06 on 16 procs for 0 steps with 9101 atoms 121.1% CPU use with 16 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 | | 4.285e-06 | | |100.00 Nlocal: 568.812 ave 603 max 548 min Histogram: 3 1 3 2 3 0 3 0 0 1 Nghost: 8650.12 ave 8737 max 8584 min Histogram: 3 1 1 1 3 3 2 1 0 1 Neighs: 303234 ave 328881 max 289458 min Histogram: 2 3 1 5 1 3 0 0 0 1 Total # of neighbors = 4851743 Ave neighs/atom = 533.09999 Ave special neighs/atom = 1.8929788 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken log 2.5_NVT.out