#------------------------------------------------------------------------------- # Stage 2.4: 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 1928 = # 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 2.4_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 2.4_instantaneous.txt restart 3000000 2.4.restart dump sci all custom 300000 2.4.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) = 0.25063947 grid = 30 30 50 stencil order = 5 estimated absolute RMS force accuracy = 0.0035059078 estimated relative force accuracy = 1.0557937e-05 using double precision KISS FFT 3d grid and FFT values/proc = 6292 1800 generated 0 of 28 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 0 2 1.00171 0.0839587 5784 2 97.4864 10.1018 1928 Per MPI rank memory allocation (min/avg/max) = 10.95 | 12.3 | 13.53 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-06 460.59246 137757.66 0.6306022 427.16581 5.1419392 9.6830219 0 0 19581.234 -2035.9551 -76.789562 -152511.07 -134950.97 5676.3721 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 9.97837e-07 5784 2 103.7 9.68891e-05 1928 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.29901e-06 5784 2 103.7 0.000103815 1928 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.36515e-06 5784 2 103.7 9.98726e-05 1928 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.09228e-06 5784 2 103.7 8.56462e-05 1928 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.25884e-06 5784 2 103.7 9.43894e-05 1928 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.30492e-06 5784 2 103.7 9.83374e-05 1928 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.09683e-06 5784 2 103.7 9.06679e-05 1928 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.41533e-06 5784 2 103.7 9.90166e-05 1928 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.69692e-06 5784 2 103.7 9.9568e-05 1928 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.25002e-06 5784 2 103.7 0.00010592 1928 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.70226e-06 5784 2 103.7 0.000121815 1928 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.29016e-06 5784 2 103.7 0.000102584 1928 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.26522e-06 5784 2 103.7 0.000123237 1928 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.20468e-06 5784 2 103.7 9.2875e-05 1928 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.07312e-06 5784 2 103.7 8.78189e-05 1928 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.097e-06 5784 2 103.7 8.83303e-05 1928 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.30818e-06 5784 2 103.7 0.000101084 1928 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.14402e-06 5784 2 103.7 8.88187e-05 1928 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.2696e-06 5784 2 103.7 8.71146e-05 1928 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.68386e-06 5784 2 103.7 0.000105099 1928 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.22164e-06 5784 2 103.7 9.86742e-05 1928 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.18335e-06 5784 2 103.7 9.62923e-05 1928 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.39816e-06 5784 2 103.7 0.00010088 1928 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.18586e-06 5784 2 103.7 0.000107637 1928 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.0743e-06 5784 2 103.7 8.88993e-05 1928 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.71959e-06 5784 2 103.7 0.00011444 1928 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.46776e-06 5784 2 103.7 0.000108638 1928 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.11245e-06 5784 2 103.7 0.000103711 1928 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.80218e-06 5784 2 103.7 0.000115632 1928 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.32837e-06 5784 2 103.7 0.00010263 1928 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.31796e-06 5784 2 103.7 0.000106348 1928 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.31187e-06 5784 2 103.7 9.05981e-05 1928 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.1709e-06 5784 2 103.7 9.79368e-05 1928 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.19733e-06 5784 2 103.7 9.97793e-05 1928 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.10398e-06 5784 2 103.7 9.20353e-05 1928 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.17382e-06 5784 2 103.7 9.77004e-05 1928 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.13124e-06 5784 2 103.7 9.39804e-05 1928 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.1975e-06 5784 2 103.7 9.03204e-05 1928 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.17376e-06 5784 2 103.7 9.35708e-05 1928 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.23456e-06 5784 2 103.7 0.0001327 1928 SHAKE stats (type/ave/delta/count) on step 2050000 2 0.97 1.28312e-06 5784 2 103.7 9.07737e-05 1928 SHAKE stats (type/ave/delta/count) on step 2100000 2 0.97 1.19829e-06 5784 2 103.7 8.6817e-05 1928 SHAKE stats (type/ave/delta/count) on step 2150000 2 0.97 1.21023e-06 5784 2 103.7 9.94486e-05 1928 SHAKE stats (type/ave/delta/count) on step 2200000 2 0.97 1.19265e-06 5784 2 103.7 8.91121e-05 1928 SHAKE stats (type/ave/delta/count) on step 2250000 2 0.97 1.5676e-06 5784 2 103.7 0.00011188 1928 SHAKE stats (type/ave/delta/count) on step 2300000 2 0.97 1.0478e-06 5784 2 103.7 9.98201e-05 1928 SHAKE stats (type/ave/delta/count) on step 2350000 2 0.97 1.27143e-06 5784 2 103.7 0.000110586 1928 SHAKE stats (type/ave/delta/count) on step 2400000 2 0.97 1.63892e-06 5784 2 103.7 0.000106403 1928 SHAKE stats (type/ave/delta/count) on step 2450000 2 0.97 1.03777e-06 5784 2 103.7 0.000110202 1928 SHAKE stats (type/ave/delta/count) on step 2500000 2 0.97 1.11908e-06 5784 2 103.7 9.68691e-05 1928 SHAKE stats (type/ave/delta/count) on step 2550000 2 0.97 1.27543e-06 5784 2 103.7 0.000121661 1928 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.97 1.48289e-06 5784 2 103.7 0.000116473 1928 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.97 1.2e-06 5784 2 103.7 9.03724e-05 1928 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.97 1.35947e-06 5784 2 103.7 0.000103508 1928 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.97 1.42988e-06 5784 2 103.7 0.000121773 1928 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.97 1.00897e-06 5784 2 103.7 9.76304e-05 1928 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.97 1.50166e-06 5784 2 103.7 9.87986e-05 1928 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.97 1.82923e-06 5784 2 103.7 0.000124071 1928 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.97 1.36603e-06 5784 2 103.7 0.000107544 1928 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.18817e-06 5784 2 103.7 9.00775e-05 1928 3000000 3000000 -327.86404 137757.66 0.6306022 297.18208 32.464164 39.394204 0 0 16317.576 11106.188 -76.789562 -152574.63 -125079.01 3949.0896 Loop time of 25126.7 on 32 procs for 3000000 steps with 6387 atoms Performance: 10.316 ns/day, 2.327 hours/ns, 119.395 timesteps/s 98.5% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.1883 | 7702.9 | 18213 |8623.2 | 30.66 Bond | 2.4414 | 5.5915 | 13.116 | 129.1 | 0.02 Kspace | 4048.5 | 14603 | 22431 |6301.2 | 58.12 Neigh | 1065.8 | 1072.2 | 1082.8 | 17.1 | 4.27 Comm | 275.87 | 650.48 | 875.44 | 850.1 | 2.59 Output | 0.011301 | 0.013223 | 0.014897 | 0.9 | 0.00 Modify | 882.12 | 1047.9 | 1287.5 | 493.7 | 4.17 Other | | 44.66 | | | 0.18 Nlocal: 199.594 ave 402 max 0 min Histogram: 12 0 3 1 0 0 0 3 1 12 Nghost: 3932.69 ave 7592 max 279 min Histogram: 4 4 0 4 4 4 3 1 4 4 Neighs: 90921.3 ave 227788 max 0 min Histogram: 16 0 0 0 0 0 5 3 4 4 Total # of neighbors = 2909481 Ave neighs/atom = 455.53171 Ave special neighs/atom = 1.8738062 Neighbor list builds = 145029 Dangerous builds = 0 undump sci restart 0 dump sci all custom 3000000 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) = 0.25063947 grid = 30 30 50 stencil order = 5 estimated absolute RMS force accuracy = 0.0035059078 estimated relative force accuracy = 1.0557937e-05 using double precision KISS FFT 3d grid and FFT values/proc = 6292 1800 generated 0 of 28 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.18817e-06 5784 2 103.7 9.00775e-05 1928 Per MPI rank memory allocation (min/avg/max) = 10.98 | 12.46 | 13.53 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 -327.41039 137757.66 0.6306022 297.18208 32.464164 39.394204 0 0 16317.576 11106.188 -76.789562 -152574.63 -125079.01 3949.0896 Loop time of 7.62378e-06 on 32 procs for 0 steps with 6387 atoms 87.7% 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 | | 7.624e-06 | | |100.00 Nlocal: 199.594 ave 402 max 0 min Histogram: 12 0 3 1 0 0 0 3 1 12 Nghost: 3932.69 ave 7592 max 279 min Histogram: 4 4 0 4 4 4 3 1 4 4 Neighs: 90921.3 ave 227788 max 0 min Histogram: 16 0 0 0 0 0 5 3 4 4 Total # of neighbors = 2909481 Ave neighs/atom = 455.53171 Ave special neighs/atom = 1.8738062 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix shaken log 2.5_NVT.out