#------------------------------------------------------------------------------- # Stage 2.5: NVT integration for 2 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 200000 200000 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 200 1 200 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 2000000 2.5.restart dump sci all custom 200000 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 2000000 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 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 = 11.5 ghost atom cutoff = 11.5 binsize = 5.75, bins = 9 9 10 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 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 SHAKE stats (type/ave/delta/count) on step 0 1 0.97 6.64802e-13 9759 2 103.7 7.4337e-11 3253 Per MPI rank memory allocation (min/avg/max) = 12.78 | 13.19 | 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 0 1e-06 92002.472 136654.71 1.2215371 296.69507 175.7555 216.50318 0 0 95452.259 36056.142 -575.21298 -390534.46 -258633.8 6882.3357 SHAKE stats (type/ave/delta/count) on step 50000 1 0.97 1.38455e-06 9759 2 103.7 0.000105308 3253 SHAKE stats (type/ave/delta/count) on step 100000 1 0.97 1.29097e-06 9759 2 103.7 0.00010104 3253 SHAKE stats (type/ave/delta/count) on step 150000 1 0.97 1.27757e-06 9759 2 103.7 8.69392e-05 3253 SHAKE stats (type/ave/delta/count) on step 200000 1 0.97 1.40039e-06 9759 2 103.7 0.00010843 3253 SHAKE stats (type/ave/delta/count) on step 250000 1 0.97 1.23944e-06 9759 2 103.7 9.01971e-05 3253 SHAKE stats (type/ave/delta/count) on step 300000 1 0.97 1.18564e-06 9759 2 103.7 0.000107917 3253 SHAKE stats (type/ave/delta/count) on step 350000 1 0.97 1.15527e-06 9759 2 103.7 9.18134e-05 3253 SHAKE stats (type/ave/delta/count) on step 400000 1 0.97 1.31906e-06 9759 2 103.7 0.000101972 3253 SHAKE stats (type/ave/delta/count) on step 450000 1 0.97 1.3075e-06 9759 2 103.7 0.000102513 3253 SHAKE stats (type/ave/delta/count) on step 500000 1 0.97 1.33471e-06 9759 2 103.7 9.49755e-05 3253 SHAKE stats (type/ave/delta/count) on step 550000 1 0.97 1.31389e-06 9759 2 103.7 9.88563e-05 3253 SHAKE stats (type/ave/delta/count) on step 600000 1 0.97 1.18276e-06 9759 2 103.7 9.81683e-05 3253 SHAKE stats (type/ave/delta/count) on step 650000 1 0.97 1.38944e-06 9759 2 103.7 0.000103895 3253 SHAKE stats (type/ave/delta/count) on step 700000 1 0.97 1.25566e-06 9759 2 103.7 0.000105263 3253 SHAKE stats (type/ave/delta/count) on step 750000 1 0.97 1.0839e-06 9759 2 103.7 9.17556e-05 3253 SHAKE stats (type/ave/delta/count) on step 800000 1 0.97 1.28533e-06 9759 2 103.7 0.000100282 3253 SHAKE stats (type/ave/delta/count) on step 850000 1 0.97 1.36696e-06 9759 2 103.7 9.73961e-05 3253 SHAKE stats (type/ave/delta/count) on step 900000 1 0.97 1.12599e-06 9759 2 103.7 8.93241e-05 3253 SHAKE stats (type/ave/delta/count) on step 950000 1 0.97 1.15777e-06 9759 2 103.7 9.4768e-05 3253 SHAKE stats (type/ave/delta/count) on step 1000000 1 0.97 1.21655e-06 9759 2 103.7 0.000101425 3253 SHAKE stats (type/ave/delta/count) on step 1050000 1 0.97 1.15773e-06 9759 2 103.7 9.15363e-05 3253 SHAKE stats (type/ave/delta/count) on step 1100000 1 0.97 1.5106e-06 9759 2 103.7 0.00010768 3253 SHAKE stats (type/ave/delta/count) on step 1150000 1 0.97 1.07796e-06 9759 2 103.7 8.86683e-05 3253 SHAKE stats (type/ave/delta/count) on step 1200000 1 0.97 1.40429e-06 9759 2 103.7 9.20928e-05 3253 SHAKE stats (type/ave/delta/count) on step 1250000 1 0.97 1.07699e-06 9759 2 103.7 0.000100175 3253 SHAKE stats (type/ave/delta/count) on step 1300000 1 0.97 1.1991e-06 9759 2 103.7 8.80617e-05 3253 SHAKE stats (type/ave/delta/count) on step 1350000 1 0.97 1.1122e-06 9759 2 103.7 9.97172e-05 3253 SHAKE stats (type/ave/delta/count) on step 1400000 1 0.97 1.19866e-06 9759 2 103.7 0.000100833 3253 SHAKE stats (type/ave/delta/count) on step 1450000 1 0.97 1.1722e-06 9759 2 103.7 9.08369e-05 3253 SHAKE stats (type/ave/delta/count) on step 1500000 1 0.97 1.56064e-06 9759 2 103.7 0.000118332 3253 SHAKE stats (type/ave/delta/count) on step 1550000 1 0.97 1.31641e-06 9759 2 103.7 9.23781e-05 3253 SHAKE stats (type/ave/delta/count) on step 1600000 1 0.97 1.15285e-06 9759 2 103.7 0.000107441 3253 SHAKE stats (type/ave/delta/count) on step 1650000 1 0.97 1.15987e-06 9759 2 103.7 0.000105046 3253 SHAKE stats (type/ave/delta/count) on step 1700000 1 0.97 1.41785e-06 9759 2 103.7 0.000101963 3253 SHAKE stats (type/ave/delta/count) on step 1750000 1 0.97 1.35304e-06 9759 2 103.7 9.38824e-05 3253 SHAKE stats (type/ave/delta/count) on step 1800000 1 0.97 1.46012e-06 9759 2 103.7 0.000100391 3253 SHAKE stats (type/ave/delta/count) on step 1850000 1 0.97 1.34033e-06 9759 2 103.7 9.88207e-05 3253 SHAKE stats (type/ave/delta/count) on step 1900000 1 0.97 1.51448e-06 9759 2 103.7 9.03984e-05 3253 SHAKE stats (type/ave/delta/count) on step 1950000 1 0.97 1.43798e-06 9759 2 103.7 0.00010949 3253 SHAKE stats (type/ave/delta/count) on step 2000000 1 0.97 1.43596e-06 9759 2 103.7 0.000110201 3253 2000000 2000000 91969.281 136654.71 1.2215371 306.11819 181.15137 243.67115 0 0 95278.362 36145.626 -575.21298 -390558.34 -258709.52 7100.9207 Loop time of 24916.4 on 32 procs for 2000000 steps with 11981 atoms Performance: 6.935 ns/day, 3.461 hours/ns, 80.268 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 | 2040.5 | 5655.9 | 7553.9 |1763.9 | 22.70 Bond | 2.5176 | 10.712 | 23.318 | 202.9 | 0.04 Kspace | 5317.7 | 7227.4 | 10875 |1576.6 | 29.01 Neigh | 434.28 | 435.78 | 438.13 | 5.6 | 1.75 Comm | 763.18 | 869.03 | 946.44 | 186.2 | 3.49 Output | 0.013024 | 0.015586 | 0.01811 | 1.2 | 0.00 Modify | 10606 | 10663 | 10726 | 37.6 | 42.79 Other | | 54.59 | | | 0.22 Nlocal: 374.406 ave 456 max 122 min Histogram: 2 0 0 0 0 1 4 15 2 8 Nghost: 5110.12 ave 5510 max 4425 min Histogram: 3 1 1 2 1 8 0 4 3 9 Neighs: 108810 ave 145145 max 27703 min Histogram: 2 0 0 0 2 6 8 5 1 8 Total # of neighbors = 3481904 Ave neighs/atom = 290.61881 Ave special neighs/atom = 1.8143728 Neighbor list builds = 99882 Dangerous builds = 0 undump sci restart 0 dump sci all custom 2000000 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) = 0.32343247 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 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 2000000 1 0.97 1.43596e-06 9759 2 103.7 0.000110201 3253 Per MPI rank memory allocation (min/avg/max) = 13.16 | 13.98 | 14.23 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 2000000 2000000 91970.039 136654.71 1.2215371 306.11819 181.15137 243.67115 0 0 95278.362 36145.626 -575.21298 -390558.34 -258709.52 7100.9207 Loop time of 8.34484e-06 on 32 procs for 0 steps with 11981 atoms 107.9% 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 | | 8.345e-06 | | |100.00 Nlocal: 374.406 ave 456 max 122 min Histogram: 2 0 0 0 0 1 4 15 2 8 Nghost: 5110.12 ave 5510 max 4425 min Histogram: 3 1 1 2 1 8 0 4 3 9 Neighs: 108810 ave 145145 max 27703 min Histogram: 2 0 0 0 2 6 8 5 1 8 Total # of neighbors = 3481904 Ave neighs/atom = 290.61881 Ave special neighs/atom = 1.8143728 Neighbor list builds = 0 Dangerous builds = 0 undump sci uncompute group_1 unfix group_1 unfix 1 unfix 2 unfix 3 unfix 4 unfix shaken Total wall time: 17:21:52