#------------------------------------------------------------------------------- # Stage 2.4: NVT integration for 1 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 100000 100000 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 100 1 100 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 1000000 2.4.restart dump sci all custom 100000 2.4.xyz id mol type q xs ys zs timestep 1 run 1000000 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 1.00088 0.0720092 8304 2 97.6643 9.85495 2768 Per MPI rank memory allocation (min/avg/max) = 14.07 | 16.31 | 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 -3032.7399 143908.11 1.3942094 410.14353 6.5923076 28.767474 0 0 32423.427 -37472.161 -320.88394 -277806.71 -282820.09 8993.151 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.3742e-06 8304 2 103.7 0.00011376 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.09264e-06 8304 2 103.7 0.000107816 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.27999e-06 8304 2 103.7 9.60782e-05 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.16683e-06 8304 2 103.7 8.75341e-05 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.177e-06 8304 2 103.7 9.72365e-05 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.97878e-06 8304 2 103.7 0.00011642 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.31419e-06 8304 2 103.7 0.000101183 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.14296e-06 8304 2 103.7 9.48326e-05 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.26519e-06 8304 2 103.7 0.000104098 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.39652e-06 8304 2 103.7 9.92421e-05 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.35017e-06 8304 2 103.7 0.000115431 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.65092e-06 8304 2 103.7 0.000110593 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.27925e-06 8304 2 103.7 8.97053e-05 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.12233e-06 8304 2 103.7 9.45269e-05 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.09312e-06 8304 2 103.7 8.87455e-05 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.57515e-06 8304 2 103.7 0.000108522 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.21284e-06 8304 2 103.7 0.000114773 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.41113e-06 8304 2 103.7 0.000103212 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.53603e-06 8304 2 103.7 9.47822e-05 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.36363e-06 8304 2 103.7 9.77633e-05 2768 1000000 1000000 -984.39296 143908.11 1.3942094 295.65385 45.945174 85.966549 0 0 29150.09 -19656.285 -320.88394 -277671.63 -268045.91 6482.7542 Loop time of 25331 on 8 procs for 1000000 steps with 10381 atoms Performance: 3.411 ns/day, 7.036 hours/ns, 39.477 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 | 2689.4 | 13607 | 20147 |5490.0 | 53.72 Bond | 1.1468 | 5.3418 | 8.8082 | 115.5 | 0.02 Kspace | 3412.8 | 9961.1 | 20889 |6423.6 | 39.32 Neigh | 995.12 | 996.21 | 997.48 | 2.9 | 3.93 Comm | 230.2 | 275.97 | 301.25 | 162.7 | 1.09 Output | 0.025477 | 0.028433 | 0.031175 | 1.1 | 0.00 Modify | 437.02 | 456.89 | 490.64 | 95.2 | 1.80 Other | | 28.81 | | | 0.11 Nlocal: 1297.62 ave 1610 max 560 min Histogram: 2 0 0 0 0 0 0 0 2 4 Nghost: 10453.8 ave 13033 max 8292 min Histogram: 2 0 0 2 2 0 0 0 0 2 Neighs: 593814 ave 845417 max 110790 min Histogram: 2 0 0 0 0 0 0 1 3 2 Total # of neighbors = 4750509 Ave neighs/atom = 457.61574 Ave special neighs/atom = 1.6595704 Neighbor list builds = 49677 Dangerous builds = 0 undump sci restart 0 dump sci all custom 1000000 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) = 0.25741609 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 1000000 2 0.97 1.36363e-06 8304 2 103.7 9.77633e-05 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 1000000 1000000 -983.87019 143908.11 1.3942094 295.65385 45.945174 85.966549 0 0 29150.09 -19656.285 -320.88394 -277671.63 -268045.91 6482.7542 Loop time of 3.20962e-06 on 8 procs for 0 steps with 10381 atoms 128.5% 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 | | 3.21e-06 | | |100.00 Nlocal: 1297.62 ave 1610 max 560 min Histogram: 2 0 0 0 0 0 0 0 2 4 Nghost: 10453.8 ave 13033 max 8292 min Histogram: 2 0 0 2 2 0 0 0 0 2 Neighs: 593814 ave 845417 max 110790 min Histogram: 2 0 0 0 0 0 0 1 3 2 Total # of neighbors = 4750509 Ave neighs/atom = 457.61574 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 2.5_NVT.out