#------------------------------------------------------------------------------- # 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 2768 = # of frozen angles find clusters CPU = 0.001 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 fix 4 fixed setforce 0.0 0.0 0.0 restart 3000000 2.5.restart dump sci all custom 300000 2.5.xyz id mol type q xs ys zs timestep 1 run 3000000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.25741609 grid = 30 30 72 stencil order = 5 estimated absolute RMS force accuracy = 0.0029011973 estimated relative force accuracy = 8.7368694e-06 using double precision KISS FFT 3d grid and FFT values/proc = 20350 8100 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 0.97 6.74794e-13 8304 2 103.7 7.24754e-11 2768 Per MPI rank memory allocation (min/avg/max) = 14.06 | 16.42 | 17.76 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 -983.86615 143908.11 1.3942094 295.65385 45.945174 85.966549 0 0 29150.09 -19656.267 -320.88394 -277671.63 -268045.9 6482.7542 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.37948e-06 8304 2 103.7 0.000101475 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.11935e-06 8304 2 103.7 9.93627e-05 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.32366e-06 8304 2 103.7 0.000100653 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.13757e-06 8304 2 103.7 9.64525e-05 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.21001e-06 8304 2 103.7 9.71364e-05 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.402e-06 8304 2 103.7 0.000102671 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.11903e-06 8304 2 103.7 0.000113941 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.10036e-06 8304 2 103.7 9.36466e-05 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.30144e-06 8304 2 103.7 9.07179e-05 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.2601e-06 8304 2 103.7 9.71951e-05 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.2477e-06 8304 2 103.7 9.62525e-05 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.06858e-06 8304 2 103.7 9.7842e-05 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.42337e-06 8304 2 103.7 9.83287e-05 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.48307e-06 8304 2 103.7 0.000111011 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.23654e-06 8304 2 103.7 0.000110676 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.27105e-06 8304 2 103.7 9.53511e-05 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.30781e-06 8304 2 103.7 0.000100221 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.15506e-06 8304 2 103.7 9.09363e-05 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.31547e-06 8304 2 103.7 9.40702e-05 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.0335e-06 8304 2 103.7 9.42096e-05 2768 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.2405e-06 8304 2 103.7 9.71176e-05 2768 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.24573e-06 8304 2 103.7 0.000108016 2768 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.18251e-06 8304 2 103.7 9.40945e-05 2768 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.20939e-06 8304 2 103.7 9.63414e-05 2768 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.71743e-06 8304 2 103.7 0.000109494 2768 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.41897e-06 8304 2 103.7 0.000107 2768 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.20532e-06 8304 2 103.7 9.05077e-05 2768 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.24133e-06 8304 2 103.7 9.54376e-05 2768 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.11718e-06 8304 2 103.7 8.89834e-05 2768 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.22438e-06 8304 2 103.7 9.5757e-05 2768 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.13144e-06 8304 2 103.7 0.000121617 2768 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.15793e-06 8304 2 103.7 9.62541e-05 2768 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.4359e-06 8304 2 103.7 0.000102096 2768 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.15989e-06 8304 2 103.7 9.23426e-05 2768 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.10184e-06 8304 2 103.7 0.000100673 2768 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.30244e-06 8304 2 103.7 8.66762e-05 2768 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.30564e-06 8304 2 103.7 9.72739e-05 2768 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.22687e-06 8304 2 103.7 9.75737e-05 2768 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.28625e-06 8304 2 103.7 9.72527e-05 2768 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.14012e-06 8304 2 103.7 9.39181e-05 2768 SHAKE stats (type/ave/delta/count) on step 2050000 2 0.97 1.46537e-06 8304 2 103.7 9.10293e-05 2768 SHAKE stats (type/ave/delta/count) on step 2100000 2 0.97 1.3422e-06 8304 2 103.7 0.000100173 2768 SHAKE stats (type/ave/delta/count) on step 2150000 2 0.97 1.47805e-06 8304 2 103.7 9.86964e-05 2768 SHAKE stats (type/ave/delta/count) on step 2200000 2 0.97 1.10604e-06 8304 2 103.7 9.86537e-05 2768 SHAKE stats (type/ave/delta/count) on step 2250000 2 0.97 1.45786e-06 8304 2 103.7 9.84884e-05 2768 SHAKE stats (type/ave/delta/count) on step 2300000 2 0.97 1.51326e-06 8304 2 103.7 0.000102634 2768 SHAKE stats (type/ave/delta/count) on step 2350000 2 0.97 1.20587e-06 8304 2 103.7 0.000101751 2768 SHAKE stats (type/ave/delta/count) on step 2400000 2 0.97 1.67212e-06 8304 2 103.7 0.000103963 2768 SHAKE stats (type/ave/delta/count) on step 2450000 2 0.97 1.12278e-06 8304 2 103.7 8.92212e-05 2768 SHAKE stats (type/ave/delta/count) on step 2500000 2 0.97 1.31829e-06 8304 2 103.7 9.86231e-05 2768 SHAKE stats (type/ave/delta/count) on step 2550000 2 0.97 1.09515e-06 8304 2 103.7 9.28447e-05 2768 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.97 1.18506e-06 8304 2 103.7 0.000100193 2768 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.97 1.26523e-06 8304 2 103.7 9.28407e-05 2768 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.97 1.21344e-06 8304 2 103.7 0.000102396 2768 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.97 1.31491e-06 8304 2 103.7 9.82279e-05 2768 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.97 1.38099e-06 8304 2 103.7 9.62679e-05 2768 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.97 1.26487e-06 8304 2 103.7 9.48209e-05 2768 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.97 1.27765e-06 8304 2 103.7 0.000119751 2768 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.97 1.19799e-06 8304 2 103.7 9.78338e-05 2768 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.55462e-06 8304 2 103.7 0.000103197 2768 3000000 3000000 -824.99694 143908.11 1.3942094 299.94307 46.410461 61.832772 0 0 29176.825 -19810.477 -320.88394 -277677.41 -268202.82 6576.8033 Loop time of 75385.8 on 8 procs for 3000000 steps with 10381 atoms Performance: 3.438 ns/day, 6.980 hours/ns, 39.795 timesteps/s 98.6% CPU use with 8 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8113.6 | 40680 | 59107 |9456.8 | 53.96 Bond | 3.3333 | 16.017 | 28.399 | 202.9 | 0.02 Kspace | 10962 | 29420 | 62026 |11131.8 | 39.03 Neigh | 2967.6 | 2971.6 | 2976.3 | 5.3 | 3.94 Comm | 688.96 | 820.54 | 892.88 | 259.9 | 1.09 Output | 0.025957 | 0.028989 | 0.031691 | 1.1 | 0.00 Modify | 1337 | 1388.1 | 1482.2 | 148.8 | 1.84 Other | | 89.01 | | | 0.12 Nlocal: 1297.62 ave 1621 max 564 min Histogram: 2 0 0 0 0 0 0 0 2 4 Nghost: 10494.4 ave 13102 max 8347 min Histogram: 2 0 0 2 2 0 0 0 0 2 Neighs: 593623 ave 846520 max 112073 min Histogram: 2 0 0 0 0 0 0 1 3 2 Total # of neighbors = 4748984 Ave neighs/atom = 457.46884 Ave special neighs/atom = 1.6595704 Neighbor list builds = 148931 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) = 0.25741609 grid = 30 30 72 stencil order = 5 estimated absolute RMS force accuracy = 0.0029011973 estimated relative force accuracy = 8.7368694e-06 using double precision KISS FFT 3d grid and FFT values/proc = 20350 8100 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.55462e-06 8304 2 103.7 0.000103197 2768 Per MPI rank memory allocation (min/avg/max) = 14.07 | 16.47 | 17.76 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 -824.32166 143908.11 1.3942094 299.94307 46.410461 61.832772 0 0 29176.825 -19810.477 -320.88394 -277677.41 -268202.82 6576.8033 Loop time of 6.51125e-06 on 8 procs for 0 steps with 10381 atoms 111.3% CPU use with 8 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 | | 6.511e-06 | | |100.00 Nlocal: 1297.62 ave 1621 max 564 min Histogram: 2 0 0 0 0 0 0 0 2 4 Nghost: 10494.4 ave 13102 max 8347 min Histogram: 2 0 0 2 2 0 0 0 0 2 Neighs: 593623 ave 846520 max 112073 min Histogram: 2 0 0 0 0 0 0 1 3 2 Total # of neighbors = 4748984 Ave neighs/atom = 457.46884 Ave special neighs/atom = 1.6595704 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix 4 unfix shaken log 2.6_Custom.out