#------------------------------------------------------------------------------- # Stage 2.5: NVT integration for 2 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 200000 200000 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 200 1 200 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 2000000 2.5.restart dump sci all custom 200000 2.5.xyz id mol type q xs ys zs timestep 1 run 2000000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.32166515 grid = 40 40 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0036376213 estimated relative force accuracy = 1.0954589e-05 using double precision KISS FFT 3d grid and FFT values/proc = 10098 3200 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 1.0029 0.110542 8304 2 97.1661 10.5551 2768 Per MPI rank memory allocation (min/avg/max) = 11.58 | 13.3 | 13.89 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 3017.7362 120303.9 1.009153 428.55654 10.041606 59.611582 0 0 27379.91 67267.702 -346.11593 -269105.87 -174388.61 8088.7858 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.10889e-06 8304 2 103.7 0.000100659 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.08937e-06 8304 2 103.7 0.000100463 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.42618e-06 8304 2 103.7 0.000106729 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.29946e-06 8304 2 103.7 9.60452e-05 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.32699e-06 8304 2 103.7 9.35516e-05 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.29778e-06 8304 2 103.7 9.33713e-05 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.49519e-06 8304 2 103.7 0.000108524 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.52761e-06 8304 2 103.7 0.000114377 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.35864e-06 8304 2 103.7 9.58187e-05 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.19105e-06 8304 2 103.7 9.1871e-05 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.14843e-06 8304 2 103.7 0.000107245 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.7616e-06 8304 2 103.7 0.000120889 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.39167e-06 8304 2 103.7 9.96481e-05 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.36878e-06 8304 2 103.7 9.79782e-05 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.78284e-06 8304 2 103.7 0.00010112 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.58023e-06 8304 2 103.7 0.000101033 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.09908e-06 8304 2 103.7 0.000107289 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.55998e-06 8304 2 103.7 0.000135839 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.49926e-06 8304 2 103.7 9.37815e-05 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.6321e-06 8304 2 103.7 0.000108555 2768 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.32069e-06 8304 2 103.7 9.41541e-05 2768 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.40347e-06 8304 2 103.7 0.000114106 2768 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.04737e-06 8304 2 103.7 9.74375e-05 2768 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.4684e-06 8304 2 103.7 9.26628e-05 2768 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.07249e-06 8304 2 103.7 9.76528e-05 2768 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.38496e-06 8304 2 103.7 0.000113217 2768 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.21517e-06 8304 2 103.7 0.000100671 2768 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.22985e-06 8304 2 103.7 0.000111301 2768 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.18938e-06 8304 2 103.7 9.33399e-05 2768 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.30955e-06 8304 2 103.7 0.000104773 2768 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.18785e-06 8304 2 103.7 0.000102121 2768 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.24168e-06 8304 2 103.7 9.68383e-05 2768 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.06025e-06 8304 2 103.7 9.18979e-05 2768 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.29701e-06 8304 2 103.7 9.92266e-05 2768 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.15822e-06 8304 2 103.7 9.26021e-05 2768 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.26013e-06 8304 2 103.7 0.000101962 2768 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.0708e-06 8304 2 103.7 9.89301e-05 2768 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.15576e-06 8304 2 103.7 9.933e-05 2768 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.16669e-06 8304 2 103.7 9.67095e-05 2768 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.03481e-06 8304 2 103.7 9.24363e-05 2768 2000000 2000000 -770.08443 120303.9 1.009153 296.46642 44.690241 69.4521 0 0 21042.89 86976.006 -346.11593 -269047.14 -160914.11 5595.6522 Loop time of 11495.6 on 32 procs for 2000000 steps with 9101 atoms Performance: 15.032 ns/day, 1.597 hours/ns, 173.980 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 | 1160.8 | 4115.2 | 5516.2 |2612.4 | 35.80 Bond | 2.0354 | 5.0456 | 8.3386 | 100.9 | 0.04 Kspace | 4316.9 | 5709.7 | 8674.3 |2227.9 | 49.67 Neigh | 322.24 | 324.15 | 326.44 | 7.2 | 2.82 Comm | 471.96 | 594.92 | 652.45 | 279.2 | 5.18 Output | 0.011901 | 0.014159 | 0.016356 | 1.1 | 0.00 Modify | 670.38 | 712.17 | 815.41 | 221.4 | 6.20 Other | | 34.45 | | | 0.30 Nlocal: 284.406 ave 365 max 57 min Histogram: 2 4 2 0 0 0 0 0 4 20 Nghost: 4163.03 ave 5140 max 3561 min Histogram: 8 2 10 4 0 0 0 0 0 8 Neighs: 76999.1 ave 108405 max 7165 min Histogram: 3 5 0 0 0 0 0 5 5 14 Total # of neighbors = 2463972 Ave neighs/atom = 270.7364 Ave special neighs/atom = 1.8929788 Neighbor list builds = 99484 Dangerous builds = 0 undump sci restart 0 dump sci all custom 2000000 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) = 0.32166515 grid = 40 40 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0036376213 estimated relative force accuracy = 1.0954589e-05 using double precision KISS FFT 3d grid and FFT values/proc = 10098 3200 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.03481e-06 8304 2 103.7 9.24363e-05 2768 Per MPI rank memory allocation (min/avg/max) = 12.69 | 13.42 | 13.88 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 -769.39227 120303.9 1.009153 296.46642 44.690241 69.4521 0 0 21042.89 86976.006 -346.11593 -269047.14 -160914.11 5595.6522 Loop time of 8.23856e-06 on 32 procs for 0 steps with 9101 atoms 113.4% 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 | | 8.239e-06 | | |100.00 Nlocal: 284.406 ave 365 max 57 min Histogram: 2 4 2 0 0 0 0 0 4 20 Nghost: 4163.03 ave 5140 max 3561 min Histogram: 8 2 10 4 0 0 0 0 0 8 Neighs: 76999.1 ave 108405 max 7165 min Histogram: 3 5 0 0 0 0 0 5 5 14 Total # of neighbors = 2463972 Ave neighs/atom = 270.7364 Ave special neighs/atom = 1.8929788 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken log 2.6_NVT.out