#------------------------------------------------------------------------------- # 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 trj all custom 30000 2.5.Trajectory.xyz id mol type q xs ys zs fix trjE all ave/time 30000 1 30000 v_etotal v_pe v_ke file 2.5.energies.txt dump sci all custom 300000 2.5.xyz id mol type q xs ys zs compute group_29 subset_Layer1 group/group subset_Layer2 pair yes kspace yes fix group_29 all ave/time 1 100 100 c_group_29 file 2.5_GroupInteractions_Layer1_Layer2_29.out compute group_30 subset_Layer1 group/group subset_Layer2 pair yes kspace no fix group_30 all ave/time 1 100 100 c_group_30 file 2.5_GroupInteractions_Layer1_Layer2_30.out compute group_31 subset_Layer1 group/group subset_Layer2 pair no kspace yes fix group_31 all ave/time 1 100 100 c_group_31 file 2.5_GroupInteractions_Layer1_Layer2_31.out timestep 1 run 3000000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.25754655 grid = 30 30 72 stencil order = 5 estimated absolute RMS force accuracy = 0.0028834269 estimated relative force accuracy = 8.6833543e-06 using double precision KISS FFT 3d grid and FFT values/proc = 7744 2700 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 14 ghost atom cutoff = 14 binsize = 7, bins = 6 6 16 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair lj/class2/coul/long, perpetual attributes: half, newton on pair build: half/bin/newton stencil: half/bin/3d bin: standard (2) compute group/group, occasional, copy from (1) attributes: half, newton on pair build: copy stencil: none bin: none (3) compute group/group, occasional, copy from (1) attributes: half, newton on pair build: copy stencil: none bin: none SHAKE stats (type/ave/delta/count) on step 0 2 0.97 6.49925e-13 8304 2 103.7 8.40998e-11 2768 Per MPI rank memory allocation (min/avg/max) = 13.71 | 14.51 | 15.02 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 -438.08728 142877.44 1.4042668 297.82969 40.294294 82.77182 0 0 29513.87 -20143.65 -323.19871 -277834.82 -268341.53 6530.4635 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.26335e-06 8304 2 103.7 9.00418e-05 2768 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.24294e-06 8304 2 103.7 0.000107897 2768 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.18272e-06 8304 2 103.7 8.79595e-05 2768 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.14363e-06 8304 2 103.7 0.000107675 2768 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.41182e-06 8304 2 103.7 0.000117516 2768 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.24956e-06 8304 2 103.7 9.19455e-05 2768 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.29691e-06 8304 2 103.7 9.29535e-05 2768 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.4987e-06 8304 2 103.7 9.24851e-05 2768 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.57254e-06 8304 2 103.7 9.7649e-05 2768 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.17518e-06 8304 2 103.7 9.81926e-05 2768 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.1097e-06 8304 2 103.7 8.76377e-05 2768 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.21087e-06 8304 2 103.7 9.27669e-05 2768 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.49795e-06 8304 2 103.7 0.000106211 2768 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.24692e-06 8304 2 103.7 9.26718e-05 2768 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.25971e-06 8304 2 103.7 9.91802e-05 2768 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.24472e-06 8304 2 103.7 9.01227e-05 2768 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.43565e-06 8304 2 103.7 9.87325e-05 2768 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.40265e-06 8304 2 103.7 0.000101294 2768 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.1798e-06 8304 2 103.7 9.39692e-05 2768 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.17947e-06 8304 2 103.7 9.1765e-05 2768 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.35586e-06 8304 2 103.7 0.000112156 2768 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.28865e-06 8304 2 103.7 9.17043e-05 2768 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.09389e-06 8304 2 103.7 9.94848e-05 2768 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.10126e-06 8304 2 103.7 8.86869e-05 2768 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.3536e-06 8304 2 103.7 9.51259e-05 2768 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.34222e-06 8304 2 103.7 0.000118291 2768 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.14906e-06 8304 2 103.7 9.73646e-05 2768 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.17567e-06 8304 2 103.7 9.61362e-05 2768 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.65363e-06 8304 2 103.7 0.000115919 2768 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.19937e-06 8304 2 103.7 9.29914e-05 2768 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.50853e-06 8304 2 103.7 9.35046e-05 2768 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.45982e-06 8304 2 103.7 9.66605e-05 2768 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.37887e-06 8304 2 103.7 0.000104035 2768 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.2191e-06 8304 2 103.7 0.000100981 2768 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.26482e-06 8304 2 103.7 0.000100259 2768 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.11481e-06 8304 2 103.7 0.000128287 2768 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.15839e-06 8304 2 103.7 9.95948e-05 2768 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.09584e-06 8304 2 103.7 9.19399e-05 2768 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.1474e-06 8304 2 103.7 9.00077e-05 2768 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.25491e-06 8304 2 103.7 9.44156e-05 2768 SHAKE stats (type/ave/delta/count) on step 2050000 2 0.97 1.21568e-06 8304 2 103.7 9.89512e-05 2768 SHAKE stats (type/ave/delta/count) on step 2100000 2 0.97 1.15872e-06 8304 2 103.7 9.60649e-05 2768 SHAKE stats (type/ave/delta/count) on step 2150000 2 0.97 1.18912e-06 8304 2 103.7 8.99931e-05 2768 SHAKE stats (type/ave/delta/count) on step 2200000 2 0.97 1.40599e-06 8304 2 103.7 0.000121102 2768 SHAKE stats (type/ave/delta/count) on step 2250000 2 0.97 1.45077e-06 8304 2 103.7 0.000115553 2768 SHAKE stats (type/ave/delta/count) on step 2300000 2 0.97 1.29204e-06 8304 2 103.7 9.7671e-05 2768 SHAKE stats (type/ave/delta/count) on step 2350000 2 0.97 1.48962e-06 8304 2 103.7 0.000112311 2768 SHAKE stats (type/ave/delta/count) on step 2400000 2 0.97 1.22762e-06 8304 2 103.7 0.000100256 2768 SHAKE stats (type/ave/delta/count) on step 2450000 2 0.97 1.30537e-06 8304 2 103.7 0.000116468 2768 SHAKE stats (type/ave/delta/count) on step 2500000 2 0.97 1.5194e-06 8304 2 103.7 9.68313e-05 2768 SHAKE stats (type/ave/delta/count) on step 2550000 2 0.97 1.30856e-06 8304 2 103.7 9.06985e-05 2768 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.97 1.34319e-06 8304 2 103.7 9.29254e-05 2768 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.97 1.68919e-06 8304 2 103.7 0.000114669 2768 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.97 1.4137e-06 8304 2 103.7 0.000101827 2768 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.97 1.56318e-06 8304 2 103.7 0.000105442 2768 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.97 1.33156e-06 8304 2 103.7 0.000106296 2768 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.97 1.11325e-06 8304 2 103.7 9.99417e-05 2768 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.97 1.57841e-06 8304 2 103.7 9.93802e-05 2768 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.97 1.34491e-06 8304 2 103.7 0.000101736 2768 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.06968e-06 8304 2 103.7 9.50711e-05 2768 3000000 3000000 -193.99655 142877.44 1.4042668 295.67223 44.478934 92.121818 0 0 29513.347 -19891.122 -323.19871 -277826.14 -268067.32 6483.1572 Loop time of 47955 on 32 procs for 3000000 steps with 10381 atoms Performance: 5.405 ns/day, 4.440 hours/ns, 62.559 timesteps/s 99.0% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2772 | 12727 | 18347 |5319.8 | 26.54 Bond | 3.354 | 9.0643 | 17.497 | 136.5 | 0.02 Kspace | 6052.6 | 11704 | 21732 |5576.6 | 24.41 Neigh | 1220.9 | 1223 | 1226.6 | 5.4 | 2.55 Comm | 1066.3 | 1508.1 | 1678.7 | 506.4 | 3.14 Output | 0.099783 | 0.12586 | 0.1518 | 4.4 | 0.00 Modify | 20559 | 20697 | 21046 | 114.1 | 43.16 Other | | 86.43 | | | 0.18 Nlocal: 324.406 ave 413 max 128 min Histogram: 6 2 0 0 0 0 1 3 3 17 Nghost: 6064.03 ave 7561 max 3894 min Histogram: 8 0 0 3 5 0 0 0 4 12 Neighs: 149470 ave 215965 max 26554 min Histogram: 8 0 0 0 0 1 4 3 0 16 Total # of neighbors = 4783051 Ave neighs/atom = 460.75051 Ave special neighs/atom = 1.6595704 Neighbor list builds = 148861 Dangerous builds = 0 undump trj unfix trjE 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) = 0.25754655 grid = 30 30 72 stencil order = 5 estimated absolute RMS force accuracy = 0.0028834269 estimated relative force accuracy = 8.6833543e-06 using double precision KISS FFT 3d grid and FFT values/proc = 7744 2700 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.06968e-06 8304 2 103.7 9.50711e-05 2768 Per MPI rank memory allocation (min/avg/max) = 13.2 | 14.98 | 16.04 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 -193.38259 142877.44 1.4042668 295.67223 44.478934 92.121818 0 0 29513.347 -19891.122 -323.19871 -277826.14 -268067.32 6483.1572 Loop time of 7.60866e-06 on 32 procs for 0 steps with 10381 atoms 117.5% 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 | | 7.609e-06 | | |100.00 Nlocal: 324.406 ave 413 max 128 min Histogram: 6 2 0 0 0 0 1 3 3 17 Nghost: 6064.03 ave 7561 max 3894 min Histogram: 8 0 0 3 5 0 0 0 4 12 Neighs: 149470 ave 215965 max 26554 min Histogram: 8 0 0 0 0 1 4 3 0 16 Total # of neighbors = 4783051 Ave neighs/atom = 460.75051 Ave special neighs/atom = 1.6595704 Neighbor list builds = 0 Dangerous builds = 0 undump sci uncompute group_29 unfix group_29 uncompute group_30 unfix group_30 uncompute group_31 unfix group_31 unfix 1 unfix 2 unfix 3 unfix 4 unfix shaken Total wall time: 15:57:47