#------------------------------------------------------------------------------- # Stage 2.4: NVT integration for 5 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 1 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 3253 = # 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 500000 500000 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 2.4_averages.txt off 1 fix 3 movable ave/time 500 1 500 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 2.4_instantaneous.txt fix 4 fixed setforce 0.0 0.0 0.0 restart 5000000 2.4.restart dump sci all custom 500000 2.4.xyz id mol type q xs ys zs timestep 1 run 5000000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.32343247 grid = 48 48 50 stencil order = 5 estimated absolute RMS force accuracy = 0.003874593 estimated relative force accuracy = 1.1668222e-05 using double precision KISS FFT 3d grid and FFT values/proc = 11191 4608 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 1 1.00449 0.133151 9759 2 97.4647 12.6236 3253 Per MPI rank memory allocation (min/avg/max) = 13 | 13.19 | 13.3 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 93971.834 136654.71 1.2215371 423.17359 32.021629 112.01697 0 0 101525.36 14095.89 -575.21298 -390856.7 -275091.42 9816.2155 SHAKE stats (type/ave/delta/count) on step 50000 1 0.97 1.65095e-06 9759 2 103.7 0.000103137 3253 SHAKE stats (type/ave/delta/count) on step 100000 1 0.97 1.38743e-06 9759 2 103.7 9.04211e-05 3253 SHAKE stats (type/ave/delta/count) on step 150000 1 0.97 1.09025e-06 9759 2 103.7 0.000100445 3253 SHAKE stats (type/ave/delta/count) on step 200000 1 0.97 1.29644e-06 9759 2 103.7 9.86476e-05 3253 SHAKE stats (type/ave/delta/count) on step 250000 1 0.97 1.23801e-06 9759 2 103.7 0.000107736 3253 SHAKE stats (type/ave/delta/count) on step 300000 1 0.97 1.20323e-06 9759 2 103.7 9.33065e-05 3253 SHAKE stats (type/ave/delta/count) on step 350000 1 0.97 1.22992e-06 9759 2 103.7 9.04555e-05 3253 SHAKE stats (type/ave/delta/count) on step 400000 1 0.97 1.42266e-06 9759 2 103.7 0.000107076 3253 SHAKE stats (type/ave/delta/count) on step 450000 1 0.97 1.45962e-06 9759 2 103.7 9.75025e-05 3253 SHAKE stats (type/ave/delta/count) on step 500000 1 0.97 1.69086e-06 9759 2 103.7 0.000156224 3253 SHAKE stats (type/ave/delta/count) on step 550000 1 0.97 1.0865e-06 9759 2 103.7 9.93503e-05 3253 SHAKE stats (type/ave/delta/count) on step 600000 1 0.97 1.36351e-06 9759 2 103.7 0.00010312 3253 SHAKE stats (type/ave/delta/count) on step 650000 1 0.97 1.40746e-06 9759 2 103.7 9.76338e-05 3253 SHAKE stats (type/ave/delta/count) on step 700000 1 0.97 1.28479e-06 9759 2 103.7 0.000108626 3253 SHAKE stats (type/ave/delta/count) on step 750000 1 0.97 1.35432e-06 9759 2 103.7 0.000100357 3253 SHAKE stats (type/ave/delta/count) on step 800000 1 0.97 1.16856e-06 9759 2 103.7 0.000116467 3253 SHAKE stats (type/ave/delta/count) on step 850000 1 0.97 1.08899e-06 9759 2 103.7 9.47841e-05 3253 SHAKE stats (type/ave/delta/count) on step 900000 1 0.97 1.18557e-06 9759 2 103.7 0.000101247 3253 SHAKE stats (type/ave/delta/count) on step 950000 1 0.97 1.41156e-06 9759 2 103.7 9.6167e-05 3253 SHAKE stats (type/ave/delta/count) on step 1000000 1 0.97 1.32531e-06 9759 2 103.7 9.84036e-05 3253 SHAKE stats (type/ave/delta/count) on step 1050000 1 0.97 1.48655e-06 9759 2 103.7 0.000111417 3253 SHAKE stats (type/ave/delta/count) on step 1100000 1 0.97 1.67765e-06 9759 2 103.7 0.000121256 3253 SHAKE stats (type/ave/delta/count) on step 1150000 1 0.97 1.16122e-06 9759 2 103.7 0.000126534 3253 SHAKE stats (type/ave/delta/count) on step 1200000 1 0.97 1.17191e-06 9759 2 103.7 9.08347e-05 3253 SHAKE stats (type/ave/delta/count) on step 1250000 1 0.97 1.14329e-06 9759 2 103.7 9.61443e-05 3253 SHAKE stats (type/ave/delta/count) on step 1300000 1 0.97 1.26755e-06 9759 2 103.7 0.000121328 3253 SHAKE stats (type/ave/delta/count) on step 1350000 1 0.97 1.08516e-06 9759 2 103.7 9.65206e-05 3253 SHAKE stats (type/ave/delta/count) on step 1400000 1 0.97 1.25312e-06 9759 2 103.7 0.000101637 3253 SHAKE stats (type/ave/delta/count) on step 1450000 1 0.97 1.2056e-06 9759 2 103.7 9.63191e-05 3253 SHAKE stats (type/ave/delta/count) on step 1500000 1 0.97 1.47379e-06 9759 2 103.7 0.000103202 3253 SHAKE stats (type/ave/delta/count) on step 1550000 1 0.97 1.16366e-06 9759 2 103.7 0.000103947 3253 SHAKE stats (type/ave/delta/count) on step 1600000 1 0.97 1.57079e-06 9759 2 103.7 0.000126286 3253 SHAKE stats (type/ave/delta/count) on step 1650000 1 0.97 1.3215e-06 9759 2 103.7 0.000106091 3253 SHAKE stats (type/ave/delta/count) on step 1700000 1 0.97 1.08211e-06 9759 2 103.7 9.4833e-05 3253 SHAKE stats (type/ave/delta/count) on step 1750000 1 0.97 1.34999e-06 9759 2 103.7 9.83354e-05 3253 SHAKE stats (type/ave/delta/count) on step 1800000 1 0.97 1.34832e-06 9759 2 103.7 0.000104245 3253 SHAKE stats (type/ave/delta/count) on step 1850000 1 0.97 1.12209e-06 9759 2 103.7 9.15848e-05 3253 SHAKE stats (type/ave/delta/count) on step 1900000 1 0.97 1.48898e-06 9759 2 103.7 9.18252e-05 3253 SHAKE stats (type/ave/delta/count) on step 1950000 1 0.97 1.16156e-06 9759 2 103.7 9.6472e-05 3253 SHAKE stats (type/ave/delta/count) on step 2000000 1 0.97 1.53474e-06 9759 2 103.7 0.000125288 3253 SHAKE stats (type/ave/delta/count) on step 2050000 1 0.97 1.3727e-06 9759 2 103.7 8.83169e-05 3253 SHAKE stats (type/ave/delta/count) on step 2100000 1 0.97 1.42521e-06 9759 2 103.7 0.000101639 3253 SHAKE stats (type/ave/delta/count) on step 2150000 1 0.97 1.69775e-06 9759 2 103.7 0.000105389 3253 SHAKE stats (type/ave/delta/count) on step 2200000 1 0.97 1.47222e-06 9759 2 103.7 9.91793e-05 3253 SHAKE stats (type/ave/delta/count) on step 2250000 1 0.97 1.19041e-06 9759 2 103.7 0.000101147 3253 SHAKE stats (type/ave/delta/count) on step 2300000 1 0.97 1.36618e-06 9759 2 103.7 8.70301e-05 3253 SHAKE stats (type/ave/delta/count) on step 2350000 1 0.97 1.24829e-06 9759 2 103.7 9.77139e-05 3253 SHAKE stats (type/ave/delta/count) on step 2400000 1 0.97 1.22879e-06 9759 2 103.7 9.7423e-05 3253 SHAKE stats (type/ave/delta/count) on step 2450000 1 0.97 1.09685e-06 9759 2 103.7 0.000104668 3253 SHAKE stats (type/ave/delta/count) on step 2500000 1 0.97 1.21446e-06 9759 2 103.7 9.49001e-05 3253 SHAKE stats (type/ave/delta/count) on step 2550000 1 0.97 1.36935e-06 9759 2 103.7 9.35688e-05 3253 SHAKE stats (type/ave/delta/count) on step 2600000 1 0.97 1.27219e-06 9759 2 103.7 0.000102729 3253 SHAKE stats (type/ave/delta/count) on step 2650000 1 0.97 1.80315e-06 9759 2 103.7 0.000119098 3253 SHAKE stats (type/ave/delta/count) on step 2700000 1 0.97 1.29897e-06 9759 2 103.7 9.58346e-05 3253 SHAKE stats (type/ave/delta/count) on step 2750000 1 0.97 1.3567e-06 9759 2 103.7 0.000109373 3253 SHAKE stats (type/ave/delta/count) on step 2800000 1 0.97 1.33109e-06 9759 2 103.7 0.000104673 3253 SHAKE stats (type/ave/delta/count) on step 2850000 1 0.97 1.148e-06 9759 2 103.7 8.84291e-05 3253 SHAKE stats (type/ave/delta/count) on step 2900000 1 0.97 1.58948e-06 9759 2 103.7 9.52801e-05 3253 SHAKE stats (type/ave/delta/count) on step 2950000 1 0.97 1.66334e-06 9759 2 103.7 0.000102899 3253 SHAKE stats (type/ave/delta/count) on step 3000000 1 0.97 1.20368e-06 9759 2 103.7 9.11665e-05 3253 SHAKE stats (type/ave/delta/count) on step 3050000 1 0.97 1.11794e-06 9759 2 103.7 0.000100699 3253 SHAKE stats (type/ave/delta/count) on step 3100000 1 0.97 1.29666e-06 9759 2 103.7 9.49946e-05 3253 SHAKE stats (type/ave/delta/count) on step 3150000 1 0.97 1.22639e-06 9759 2 103.7 9.16818e-05 3253 SHAKE stats (type/ave/delta/count) on step 3200000 1 0.97 1.08193e-06 9759 2 103.7 9.32154e-05 3253 SHAKE stats (type/ave/delta/count) on step 3250000 1 0.97 2.04263e-06 9759 2 103.7 0.000129108 3253 SHAKE stats (type/ave/delta/count) on step 3300000 1 0.97 1.18492e-06 9759 2 103.7 0.000109951 3253 SHAKE stats (type/ave/delta/count) on step 3350000 1 0.97 1.57973e-06 9759 2 103.7 0.000111424 3253 SHAKE stats (type/ave/delta/count) on step 3400000 1 0.97 1.65575e-06 9759 2 103.7 0.000129105 3253 SHAKE stats (type/ave/delta/count) on step 3450000 1 0.97 1.33932e-06 9759 2 103.7 9.20604e-05 3253 SHAKE stats (type/ave/delta/count) on step 3500000 1 0.97 1.18831e-06 9759 2 103.7 9.34721e-05 3253 SHAKE stats (type/ave/delta/count) on step 3550000 1 0.97 1.81301e-06 9759 2 103.7 0.000126122 3253 SHAKE stats (type/ave/delta/count) on step 3600000 1 0.97 1.22901e-06 9759 2 103.7 9.56029e-05 3253 SHAKE stats (type/ave/delta/count) on step 3650000 1 0.97 1.40308e-06 9759 2 103.7 0.000100099 3253 SHAKE stats (type/ave/delta/count) on step 3700000 1 0.97 1.19377e-06 9759 2 103.7 0.000102659 3253 SHAKE stats (type/ave/delta/count) on step 3750000 1 0.97 1.58309e-06 9759 2 103.7 9.96974e-05 3253 SHAKE stats (type/ave/delta/count) on step 3800000 1 0.97 1.22674e-06 9759 2 103.7 9.93252e-05 3253 SHAKE stats (type/ave/delta/count) on step 3850000 1 0.97 1.28822e-06 9759 2 103.7 9.58697e-05 3253 SHAKE stats (type/ave/delta/count) on step 3900000 1 0.97 1.18732e-06 9759 2 103.7 9.41248e-05 3253 SHAKE stats (type/ave/delta/count) on step 3950000 1 0.97 1.78735e-06 9759 2 103.7 0.000108908 3253 SHAKE stats (type/ave/delta/count) on step 4000000 1 0.97 1.19282e-06 9759 2 103.7 0.000103743 3253 SHAKE stats (type/ave/delta/count) on step 4050000 1 0.97 1.29588e-06 9759 2 103.7 9.4274e-05 3253 SHAKE stats (type/ave/delta/count) on step 4100000 1 0.97 1.39587e-06 9759 2 103.7 0.00010511 3253 SHAKE stats (type/ave/delta/count) on step 4150000 1 0.97 1.74748e-06 9759 2 103.7 0.000119229 3253 SHAKE stats (type/ave/delta/count) on step 4200000 1 0.97 1.12827e-06 9759 2 103.7 9.90925e-05 3253 SHAKE stats (type/ave/delta/count) on step 4250000 1 0.97 1.19614e-06 9759 2 103.7 0.000104169 3253 SHAKE stats (type/ave/delta/count) on step 4300000 1 0.97 1.35809e-06 9759 2 103.7 0.000103791 3253 SHAKE stats (type/ave/delta/count) on step 4350000 1 0.97 1.56059e-06 9759 2 103.7 0.00010193 3253 SHAKE stats (type/ave/delta/count) on step 4400000 1 0.97 1.12672e-06 9759 2 103.7 0.000101841 3253 SHAKE stats (type/ave/delta/count) on step 4450000 1 0.97 1.27058e-06 9759 2 103.7 9.30709e-05 3253 SHAKE stats (type/ave/delta/count) on step 4500000 1 0.97 1.5039e-06 9759 2 103.7 9.67744e-05 3253 SHAKE stats (type/ave/delta/count) on step 4550000 1 0.97 1.17946e-06 9759 2 103.7 9.63508e-05 3253 SHAKE stats (type/ave/delta/count) on step 4600000 1 0.97 1.32509e-06 9759 2 103.7 0.000103583 3253 SHAKE stats (type/ave/delta/count) on step 4650000 1 0.97 1.18349e-06 9759 2 103.7 8.94275e-05 3253 SHAKE stats (type/ave/delta/count) on step 4700000 1 0.97 1.46192e-06 9759 2 103.7 0.000105523 3253 SHAKE stats (type/ave/delta/count) on step 4750000 1 0.97 1.24873e-06 9759 2 103.7 9.59688e-05 3253 SHAKE stats (type/ave/delta/count) on step 4800000 1 0.97 1.109e-06 9759 2 103.7 9.11579e-05 3253 SHAKE stats (type/ave/delta/count) on step 4850000 1 0.97 1.29664e-06 9759 2 103.7 0.000102694 3253 SHAKE stats (type/ave/delta/count) on step 4900000 1 0.97 1.30822e-06 9759 2 103.7 0.000102038 3253 SHAKE stats (type/ave/delta/count) on step 4950000 1 0.97 1.15322e-06 9759 2 103.7 0.00010265 3253 SHAKE stats (type/ave/delta/count) on step 5000000 1 0.97 1.46126e-06 9759 2 103.7 0.000119382 3253 5000000 5000000 92001.76 136654.71 1.2215371 296.69507 175.7555 216.50318 0 0 95452.259 36056.125 -575.21298 -390534.46 -258633.82 6882.3357 Loop time of 37584.8 on 32 procs for 5000000 steps with 11981 atoms Performance: 11.494 ns/day, 2.088 hours/ns, 133.033 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 | 6217.1 | 14132 | 18930 |2710.1 | 37.60 Bond | 5.5136 | 24.255 | 55.904 | 335.9 | 0.06 Kspace | 13046 | 17899 | 25903 |2434.3 | 47.62 Neigh | 1078.4 | 1083.4 | 1089.3 | 9.0 | 2.88 Comm | 1683.1 | 1943 | 2124.3 | 314.5 | 5.17 Output | 0.013314 | 0.015972 | 0.018565 | 1.3 | 0.00 Modify | 2248.1 | 2390.8 | 2563.7 | 194.4 | 6.36 Other | | 112.6 | | | 0.30 Nlocal: 374.406 ave 471 max 126 min Histogram: 1 1 0 0 0 4 3 15 0 8 Nghost: 5120.16 ave 5511 max 4444 min Histogram: 4 0 1 2 5 1 3 2 4 10 Neighs: 109146 ave 152278 max 27888 min Histogram: 1 1 0 2 2 5 7 6 1 7 Total # of neighbors = 3492656 Ave neighs/atom = 291.51623 Ave special neighs/atom = 1.8143728 Neighbor list builds = 249568 Dangerous builds = 0 undump sci restart 0 dump sci all custom 5000000 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) = 0.32343247 grid = 48 48 50 stencil order = 5 estimated absolute RMS force accuracy = 0.003874593 estimated relative force accuracy = 1.1668222e-05 using double precision KISS FFT 3d grid and FFT values/proc = 11191 4608 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 5000000 1 0.97 1.46126e-06 9759 2 103.7 0.000119382 3253 Per MPI rank memory allocation (min/avg/max) = 13.16 | 13.29 | 13.47 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 5000000 5000000 92002.469 136654.71 1.2215371 296.69507 175.7555 216.50318 0 0 95452.259 36056.125 -575.21298 -390534.46 -258633.82 6882.3357 Loop time of 8.1155e-06 on 32 procs for 0 steps with 11981 atoms 115.5% 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 | | 8.115e-06 | | |100.00 Nlocal: 374.406 ave 471 max 126 min Histogram: 1 1 0 0 0 4 3 15 0 8 Nghost: 5120.16 ave 5511 max 4444 min Histogram: 4 0 1 2 5 1 3 2 4 10 Neighs: 109146 ave 152278 max 27888 min Histogram: 1 1 0 2 2 5 7 6 1 7 Total # of neighbors = 3492656 Ave neighs/atom = 291.51623 Ave special neighs/atom = 1.8143728 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix 4 unfix shaken log 2.5_NVT.out