#------------------------------------------------------------------------------- # 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 2297 = # 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 restart 3000000 2.5.restart dump sci all custom 300000 2.5.xyz id mol type q xs ys zs compute group_1 subset_Layer1 group/group subset_Layer2 pair yes kspace yes fix group_1 all ave/time 1 100 100 c_group_1 file 2.5_GroupInteractions_Layer1_Layer2_1.out timestep 1 run 3000000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.26028481 grid = 25 24 72 stencil order = 5 estimated absolute RMS force accuracy = 0.0025861148 estimated relative force accuracy = 7.788008e-06 using double precision KISS FFT 3d grid and FFT values/proc = 5776 1800 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule WARNING: Both groups in compute group/group have a net charge; the Kspace boundary correction to energy will be non-zero (../compute_group_group.cpp:140) 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 = 5 4 17 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) pair lj/class2/coul/long, perpetual attributes: half, newton on pair build: half/bin/newton/tri stencil: half/bin/3d/tri bin: standard (2) 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 3.6188e-09 6891 2 103.7 4.02498e-07 2297 Per MPI rank memory allocation (min/avg/max) = 12.86 | 12.96 | 13.1 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 -395.90435 80971.351 1.3313813 294.64235 123.13061 148.85575 0 0 19715.814 21018.865 -203.60435 -201432.34 -160425.67 4841.9183 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.46804e-06 6891 2 103.7 8.99947e-05 2297 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.50377e-06 6891 2 103.7 0.000118908 2297 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.44192e-06 6891 2 103.7 0.000107919 2297 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.14867e-06 6891 2 103.7 9.5167e-05 2297 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.36636e-06 6891 2 103.7 9.46042e-05 2297 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.10108e-06 6891 2 103.7 0.000103427 2297 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.29949e-06 6891 2 103.7 8.76814e-05 2297 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.25109e-06 6891 2 103.7 9.06796e-05 2297 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.69729e-06 6891 2 103.7 0.000159318 2297 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.3753e-06 6891 2 103.7 0.000107565 2297 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.22061e-06 6891 2 103.7 8.97047e-05 2297 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.32068e-06 6891 2 103.7 0.000101026 2297 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.25689e-06 6891 2 103.7 0.00010487 2297 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.04963e-06 6891 2 103.7 9.87149e-05 2297 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.18151e-06 6891 2 103.7 0.000116687 2297 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.34355e-06 6891 2 103.7 0.000112926 2297 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.05236e-06 6891 2 103.7 9.21677e-05 2297 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.41844e-06 6891 2 103.7 9.85443e-05 2297 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.20108e-06 6891 2 103.7 9.35698e-05 2297 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.52392e-06 6891 2 103.7 0.000119825 2297 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.28375e-06 6891 2 103.7 0.000116758 2297 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.65138e-06 6891 2 103.7 0.000112169 2297 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.40296e-06 6891 2 103.7 0.000100488 2297 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.22884e-06 6891 2 103.7 0.000112756 2297 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.09507e-06 6891 2 103.7 8.81297e-05 2297 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.67668e-06 6891 2 103.7 0.000107251 2297 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.33945e-06 6891 2 103.7 9.69333e-05 2297 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.63076e-06 6891 2 103.7 0.000120496 2297 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.19457e-06 6891 2 103.7 9.06851e-05 2297 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.3289e-06 6891 2 103.7 0.000106428 2297 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.86253e-06 6891 2 103.7 0.00010371 2297 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.23493e-06 6891 2 103.7 0.000104075 2297 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.18778e-06 6891 2 103.7 0.000104102 2297 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.19444e-06 6891 2 103.7 8.69197e-05 2297 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.60907e-06 6891 2 103.7 0.000102274 2297 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.27446e-06 6891 2 103.7 9.43293e-05 2297 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.23543e-06 6891 2 103.7 9.80877e-05 2297 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.06148e-06 6891 2 103.7 8.78079e-05 2297 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.42685e-06 6891 2 103.7 0.000100936 2297 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.12081e-06 6891 2 103.7 9.01869e-05 2297 SHAKE stats (type/ave/delta/count) on step 2050000 2 0.97 1.78733e-06 6891 2 103.7 0.000132461 2297 SHAKE stats (type/ave/delta/count) on step 2100000 2 0.97 1.43903e-06 6891 2 103.7 0.0001146 2297 SHAKE stats (type/ave/delta/count) on step 2150000 2 0.97 1.2044e-06 6891 2 103.7 0.000106764 2297 SHAKE stats (type/ave/delta/count) on step 2200000 2 0.97 1.02366e-06 6891 2 103.7 9.84396e-05 2297 SHAKE stats (type/ave/delta/count) on step 2250000 2 0.97 1.24945e-06 6891 2 103.7 9.14473e-05 2297 SHAKE stats (type/ave/delta/count) on step 2300000 2 0.97 1.46948e-06 6891 2 103.7 0.000116843 2297 SHAKE stats (type/ave/delta/count) on step 2350000 2 0.97 1.37825e-06 6891 2 103.7 0.000102762 2297 SHAKE stats (type/ave/delta/count) on step 2400000 2 0.97 1.45045e-06 6891 2 103.7 0.000109058 2297 SHAKE stats (type/ave/delta/count) on step 2450000 2 0.97 1.50327e-06 6891 2 103.7 8.9454e-05 2297 SHAKE stats (type/ave/delta/count) on step 2500000 2 0.97 1.42538e-06 6891 2 103.7 0.000102557 2297 SHAKE stats (type/ave/delta/count) on step 2550000 2 0.97 1.64242e-06 6891 2 103.7 9.3895e-05 2297 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.97 1.14244e-06 6891 2 103.7 8.56725e-05 2297 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.97 1.78998e-06 6891 2 103.7 0.000119947 2297 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.97 1.18742e-06 6891 2 103.7 9.78448e-05 2297 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.97 1.30506e-06 6891 2 103.7 0.000105223 2297 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.97 1.53448e-06 6891 2 103.7 9.76823e-05 2297 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.97 1.28279e-06 6891 2 103.7 9.61084e-05 2297 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.97 1.35993e-06 6891 2 103.7 9.2263e-05 2297 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.97 1.19768e-06 6891 2 103.7 9.52817e-05 2297 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.22105e-06 6891 2 103.7 0.000102695 2297 3000000 3000000 577.17089 80971.351 1.3313813 300.98309 120.82328 156.36816 0 0 19904.651 20816.127 -203.60435 -201452.63 -160454.66 4946.1171 Loop time of 34732.4 on 32 procs for 3000000 steps with 7811 atoms Performance: 7.463 ns/day, 3.216 hours/ns, 86.375 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 | 10551 | 11934 | 15749 |1358.8 | 34.36 Bond | 4.0554 | 13.223 | 37.359 | 273.9 | 0.04 Kspace | 4290.6 | 8160.9 | 9561.1 |1662.9 | 23.50 Neigh | 1096 | 1099.3 | 1102.6 | 5.4 | 3.16 Comm | 1413.1 | 1500.1 | 1625.7 | 167.4 | 4.32 Output | 0.010782 | 0.012827 | 0.014736 | 1.1 | 0.00 Modify | 11848 | 11941 | 12008 | 46.7 | 34.38 Other | | 84.23 | | | 0.24 Nlocal: 244.094 ave 287 max 215 min Histogram: 1 4 8 8 3 4 0 0 0 4 Nghost: 6714.88 ave 7199 max 6301 min Histogram: 3 8 5 3 1 0 0 3 2 7 Neighs: 135760 ave 181822 max 113622 min Histogram: 5 4 12 5 2 0 0 0 0 4 Total # of neighbors = 4344318 Ave neighs/atom = 556.17949 Ave special neighs/atom = 1.9743951 Neighbor list builds = 144672 Dangerous builds = 0 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) = 0.26028481 grid = 25 24 72 stencil order = 5 estimated absolute RMS force accuracy = 0.0025861148 estimated relative force accuracy = 7.788008e-06 using double precision KISS FFT 3d grid and FFT values/proc = 5776 1800 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule WARNING: Both groups in compute group/group have a net charge; the Kspace boundary correction to energy will be non-zero (../compute_group_group.cpp:140) SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.22105e-06 6891 2 103.7 0.000102695 2297 Per MPI rank memory allocation (min/avg/max) = 13.63 | 13.8 | 14.62 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 578.30144 80971.351 1.3313813 300.98309 120.82328 156.36816 0 0 19904.651 20816.127 -203.60435 -201452.63 -160454.66 4946.1171 Loop time of 8.24325e-06 on 32 procs for 0 steps with 7811 atoms 113.7% 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 | | 8.243e-06 | | |100.00 Nlocal: 244.094 ave 287 max 215 min Histogram: 1 4 8 8 3 4 0 0 0 4 Nghost: 6714.88 ave 7199 max 6301 min Histogram: 3 8 5 3 1 0 0 3 2 7 Neighs: 135760 ave 181822 max 113622 min Histogram: 5 4 12 5 2 0 0 0 0 4 Total # of neighbors = 4344318 Ave neighs/atom = 556.17949 Ave special neighs/atom = 1.9743951 Neighbor list builds = 0 Dangerous builds = 0 undump sci uncompute group_1 unfix group_1 unfix 1 unfix 2 unfix 3 unfix shaken Total wall time: 16:37:35