#------------------------------------------------------------------------------- # Stage 2.5: NVT integration for 3 ns with a timestep of 1 fs # Temperature 298.2 K #------------------------------------------------------------------------------- # 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 3472 = # of frozen angles find clusters CPU = 0.002 seconds 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 fix 1 movable nvt temp 298.2 298.2 100 drag 0.0 fix 2 movable ave/time 1 300000 300000 v_time c_thermo_temp c_thermo_press v_sysvol v_sysdensity v_etotal 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 300 1 300 v_time c_thermo_temp c_thermo_press v_sysvol v_sysdensity v_etotal 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 3000000 2.5.restart dump sci all custom 300000 2.5.xyz id mol type q xs ys zs compute group_1 subset_solution2 group/group subset_kainite pair yes kspace yes fix group_1 all ave/time 1 100 100 c_group_1 file 2.5_GroupInteractions_solution2_kainite_1.out timestep 1 run 3000000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.26065044 grid = 36 36 64 stencil order = 5 estimated absolute RMS force accuracy = 0.0028849559 estimated relative force accuracy = 8.6879589e-06 using double precision KISS FFT 3d grid and FFT values/proc = 9375 2592 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule WARNING: Both groups in compute group/group have a net charge; the Kspace boundary correction to energy will be non-zero (../compute_group_group.cpp:140) 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 = 7 6 15 2 neighbor lists, perpetual/occasional/extra = 1 1 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 (2) compute group/group, occasional, copy from (1) attributes: half, newton on pair build: copy stencil: none bin: none SHAKE stats (type/ave/delta/count) on step 0 2 0.97 9.36496e-10 10416 2 103.7 1.0444e-07 3472 Per MPI rank memory allocation (min/avg/max) = 13.44 | 13.65 | 13.85 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 1929.468 146737.03 1.5355781 295.70839 447.24654 569.57269 0 0 40502.014 -34292.476 -443.96083 -406123.2 -398896.84 8627.6379 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.22515e-06 10416 2 103.7 9.79376e-05 3472 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.17852e-06 10416 2 103.7 9.98355e-05 3472 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.2367e-06 10416 2 103.7 9.48737e-05 3472 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.25215e-06 10416 2 103.7 9.30911e-05 3472 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.15004e-06 10416 2 103.7 9.38922e-05 3472 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.68569e-06 10416 2 103.7 0.000101495 3472 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.3541e-06 10416 2 103.7 0.000120456 3472 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.16133e-06 10416 2 103.7 9.52966e-05 3472 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.61755e-06 10416 2 103.7 0.000118259 3472 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.24017e-06 10416 2 103.7 9.58717e-05 3472 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.36042e-06 10416 2 103.7 0.000103101 3472 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.70686e-06 10416 2 103.7 9.44774e-05 3472 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.46668e-06 10416 2 103.7 0.00011138 3472 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.24497e-06 10416 2 103.7 9.39337e-05 3472 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.52619e-06 10416 2 103.7 0.00010538 3472 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.21667e-06 10416 2 103.7 9.64818e-05 3472 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.35149e-06 10416 2 103.7 9.54845e-05 3472 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.3186e-06 10416 2 103.7 0.000101735 3472 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.23725e-06 10416 2 103.7 0.000102315 3472 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.29369e-06 10416 2 103.7 0.000100181 3472 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.31024e-06 10416 2 103.7 9.33668e-05 3472 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.44007e-06 10416 2 103.7 0.000117281 3472 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.21567e-06 10416 2 103.7 9.35086e-05 3472 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.33725e-06 10416 2 103.7 9.46389e-05 3472 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.2612e-06 10416 2 103.7 0.000100775 3472 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.13157e-06 10416 2 103.7 9.75293e-05 3472 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.41085e-06 10416 2 103.7 9.26058e-05 3472 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.29034e-06 10416 2 103.7 0.000118349 3472 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.25719e-06 10416 2 103.7 9.25783e-05 3472 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.23427e-06 10416 2 103.7 9.65972e-05 3472 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.51156e-06 10416 2 103.7 0.000118809 3472 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.36977e-06 10416 2 103.7 9.26409e-05 3472 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.47546e-06 10416 2 103.7 0.00010199 3472 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.38174e-06 10416 2 103.7 0.000106916 3472 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.28408e-06 10416 2 103.7 9.73351e-05 3472 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.30216e-06 10416 2 103.7 0.000105518 3472 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.29456e-06 10416 2 103.7 0.000107782 3472 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.25269e-06 10416 2 103.7 9.18936e-05 3472 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.39794e-06 10416 2 103.7 9.44378e-05 3472 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.76024e-06 10416 2 103.7 9.64396e-05 3472 SHAKE stats (type/ave/delta/count) on step 2050000 2 0.97 1.18547e-06 10416 2 103.7 0.00010106 3472 SHAKE stats (type/ave/delta/count) on step 2100000 2 0.97 1.18849e-06 10416 2 103.7 0.000106385 3472 SHAKE stats (type/ave/delta/count) on step 2150000 2 0.97 1.21364e-06 10416 2 103.7 9.79051e-05 3472 SHAKE stats (type/ave/delta/count) on step 2200000 2 0.97 1.10263e-06 10416 2 103.7 9.48512e-05 3472 SHAKE stats (type/ave/delta/count) on step 2250000 2 0.97 1.45458e-06 10416 2 103.7 0.000104265 3472 SHAKE stats (type/ave/delta/count) on step 2300000 2 0.97 1.22508e-06 10416 2 103.7 9.37378e-05 3472 SHAKE stats (type/ave/delta/count) on step 2350000 2 0.97 1.55348e-06 10416 2 103.7 9.61821e-05 3472 SHAKE stats (type/ave/delta/count) on step 2400000 2 0.97 1.23151e-06 10416 2 103.7 9.47631e-05 3472 SHAKE stats (type/ave/delta/count) on step 2450000 2 0.97 1.6694e-06 10416 2 103.7 0.000102644 3472 SHAKE stats (type/ave/delta/count) on step 2500000 2 0.97 1.477e-06 10416 2 103.7 0.000114902 3472 SHAKE stats (type/ave/delta/count) on step 2550000 2 0.97 1.16391e-06 10416 2 103.7 9.80891e-05 3472 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.97 1.73343e-06 10416 2 103.7 0.000120855 3472 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.97 1.26323e-06 10416 2 103.7 9.94973e-05 3472 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.97 1.2308e-06 10416 2 103.7 9.44245e-05 3472 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.97 1.30633e-06 10416 2 103.7 9.76568e-05 3472 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.97 1.16843e-06 10416 2 103.7 9.53452e-05 3472 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.97 1.11393e-06 10416 2 103.7 9.64078e-05 3472 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.97 1.34886e-06 10416 2 103.7 0.000108316 3472 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.97 1.1616e-06 10416 2 103.7 9.63686e-05 3472 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.20206e-06 10416 2 103.7 9.79519e-05 3472 3000000 3000000 1731.8674 146737.03 1.5355781 297.7916 460.94592 556.4861 0 0 40684.88 -34694.14 -443.96083 -406089.44 -399081.27 8688.4179 Loop time of 50558.3 on 32 procs for 3000000 steps with 13261 atoms Performance: 5.127 ns/day, 4.681 hours/ns, 59.337 timesteps/s 99.1% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 16187 | 18767 | 20477 |1067.0 | 37.12 Bond | 5.7301 | 30.061 | 70.55 | 445.0 | 0.06 Kspace | 7307.8 | 9000.5 | 11562 |1529.7 | 17.80 Neigh | 1420.1 | 1421.7 | 1423.1 | 2.3 | 2.81 Comm | 2035.1 | 2159.9 | 2239.3 | 133.8 | 4.27 Output | 0.01449 | 0.017363 | 0.020102 | 1.3 | 0.00 Modify | 19017 | 19075 | 19163 | 35.6 | 37.73 Other | | 104.1 | | | 0.21 Nlocal: 414.406 ave 445 max 382 min Histogram: 4 3 1 4 1 3 7 4 2 3 Nghost: 7770.28 ave 7998 max 7494 min Histogram: 7 1 0 3 4 1 1 3 6 6 Neighs: 215685 ave 239567 max 185065 min Histogram: 5 3 0 0 1 4 6 3 9 1 Total # of neighbors = 6901914 Ave neighs/atom = 520.46708 Ave special neighs/atom = 2.0037705 Neighbor list builds = 149451 Dangerous builds = 0 undump sci restart 0 dump sci all custom 3000000 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) = 0.26065044 grid = 36 36 64 stencil order = 5 estimated absolute RMS force accuracy = 0.0028849559 estimated relative force accuracy = 8.6879589e-06 using double precision KISS FFT 3d grid and FFT values/proc = 9375 2592 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule WARNING: Both groups in compute group/group have a net charge; the Kspace boundary correction to energy will be non-zero (../compute_group_group.cpp:140) SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.20206e-06 10416 2 103.7 9.79519e-05 3472 Per MPI rank memory allocation (min/avg/max) = 14.76 | 14.89 | 14.99 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 1732.7837 146737.03 1.5355781 297.7916 460.94592 556.4861 0 0 40684.88 -34694.14 -443.96083 -406089.44 -399081.27 8688.4179 Loop time of 1.07287e-05 on 32 procs for 0 steps with 13261 atoms 112.4% 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 | | 1.073e-05 | | |100.00 Nlocal: 414.406 ave 445 max 382 min Histogram: 4 3 1 4 1 3 7 4 2 3 Nghost: 7770.28 ave 7998 max 7494 min Histogram: 7 1 0 3 4 1 1 3 6 6 Neighs: 215685 ave 239567 max 185065 min Histogram: 5 3 0 0 1 4 6 3 9 1 Total # of neighbors = 6901914 Ave neighs/atom = 520.46708 Ave special neighs/atom = 2.0037705 Neighbor list builds = 0 Dangerous builds = 0 undump sci uncompute group_1 unfix group_1 unfix 1 unfix 2 unfix 3 unfix shaken Total wall time: 24:05:55