#------------------------------------------------------------------------------- # Stage 2.5: NVT integration for 10 ps 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 2812 = # 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 1000 1000 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 1 1 1 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 10000 2.5.restart dump trj all custom 100 2.5.Trajectory.xyz id mol type q xs ys zs fix trjE all ave/time 100 1 100 v_etotal v_pe v_ke file 2.5.energies.txt dump sci all custom 1000 2.5.xyz id mol type q xs ys zs compute group_15 subset_layer2 group/group subset_Li_1 pair yes kspace yes fix group_15 all ave/time 1 100 100 c_group_15 file 2.5_GroupInteractions_layer2_Li_1_15.out compute group_16 subset_layer2 group/group subset_Na_1 pair yes kspace yes fix group_16 all ave/time 1 100 100 c_group_16 file 2.5_GroupInteractions_layer2_Na_1_16.out compute group_17 subset_layer2 group/group subset_Cl_1 pair yes kspace yes fix group_17 all ave/time 1 100 100 c_group_17 file 2.5_GroupInteractions_layer2_Cl_1_17.out compute group_18 subset_layer2 group/group subset_K_1 pair yes kspace yes fix group_18 all ave/time 1 100 100 c_group_18 file 2.5_GroupInteractions_layer2_K_1_18.out compute group_19 subset_layer2 group/group subset_Mg_1 pair yes kspace yes fix group_19 all ave/time 1 100 100 c_group_19 file 2.5_GroupInteractions_layer2_Mg_1_19.out compute group_20 subset_layer2 group/group subset_SO4_1 pair yes kspace yes fix group_20 all ave/time 1 100 100 c_group_20 file 2.5_GroupInteractions_layer2_SO4_1_20.out compute group_21 subset_layer2 group/group subset_H2O_1 pair yes kspace yes fix group_21 all ave/time 1 100 100 c_group_21 file 2.5_GroupInteractions_layer2_H2O_1_21.out timestep 1 run 10000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.25537807 grid = 30 30 64 stencil order = 5 estimated absolute RMS force accuracy = 0.0034433421 estimated relative force accuracy = 1.0369522e-05 using double precision KISS FFT 3d grid and FFT values/proc = 7260 1800 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 15 8 neighbor lists, perpetual/occasional/extra = 1 7 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 (4) compute group/group, occasional, copy from (1) attributes: half, newton on pair build: copy stencil: none bin: none (5) compute group/group, occasional, copy from (1) attributes: half, newton on pair build: copy stencil: none bin: none (6) compute group/group, occasional, copy from (1) attributes: half, newton on pair build: copy stencil: none bin: none (7) compute group/group, occasional, copy from (1) attributes: half, newton on pair build: copy stencil: none bin: none (8) 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 6.48037e-13 8436 2 103.7 7.71223e-11 2812 Per MPI rank memory allocation (min/avg/max) = 13.73 | 14.45 | 14.92 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 -79.123805 141184.09 1.4079299 294.32343 41.895329 79.032406 0 0 32157.224 -35746.762 -312.04795 -284049.43 -287518.04 6729.939 10000 10000 -131.42785 141184.09 1.4079299 298.63458 48.196594 76.721877 0 0 32049.708 -35714.676 -312.04795 -284059.96 -287600 6828.5166 Loop time of 236.405 on 32 procs for 10000 steps with 10808 atoms Performance: 3.655 ns/day, 6.567 hours/ns, 42.300 timesteps/s 99.1% CPU use with 32 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 12.874 | 45.41 | 64.905 | 284.7 | 19.21 Bond | 0.012447 | 0.033438 | 0.072041 | 9.8 | 0.01 Kspace | 16.576 | 36.183 | 68.995 | 320.6 | 15.31 Neigh | 4.334 | 4.3503 | 4.3738 | 0.6 | 1.84 Comm | 3.8768 | 5.2805 | 5.8218 | 26.4 | 2.23 Output | 0.10289 | 0.12924 | 0.15532 | 4.3 | 0.05 Modify | 144.26 | 144.69 | 145.77 | 4.1 | 61.20 Other | | 0.3334 | | | 0.14 Nlocal: 337.75 ave 429 max 160 min Histogram: 4 4 0 0 0 0 0 7 9 8 Nghost: 6424.38 ave 7710 max 4734 min Histogram: 8 0 0 4 4 0 0 0 4 12 Neighs: 158559 ave 231599 max 43058 min Histogram: 8 0 0 0 0 4 1 3 12 4 Total # of neighbors = 5073881 Ave neighs/atom = 469.45605 Ave special neighs/atom = 1.6184308 Neighbor list builds = 493 Dangerous builds = 0 undump trj unfix trjE undump sci restart 0 dump sci all custom 10000 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) = 0.25537807 grid = 30 30 64 stencil order = 5 estimated absolute RMS force accuracy = 0.0034433421 estimated relative force accuracy = 1.0369522e-05 using double precision KISS FFT 3d grid and FFT values/proc = 7260 1800 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 10000 2 0.97 1.24334e-06 8436 2 103.7 9.12659e-05 2812 Per MPI rank memory allocation (min/avg/max) = 15.13 | 19.18 | 21.66 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 10000 10000 -130.88791 141184.09 1.4079299 298.63458 48.196594 76.721877 0 0 32049.708 -35714.676 -312.04795 -284059.96 -287600 6828.5166 Loop time of 1.4154e-05 on 32 procs for 0 steps with 10808 atoms 103.3% 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 | | 1.415e-05 | | |100.00 Nlocal: 337.75 ave 429 max 160 min Histogram: 4 4 0 0 0 0 0 7 9 8 Nghost: 6424.38 ave 7710 max 4734 min Histogram: 8 0 0 4 4 0 0 0 4 12 Neighs: 158559 ave 231599 max 43058 min Histogram: 8 0 0 0 0 4 1 3 12 4 Total # of neighbors = 5073881 Ave neighs/atom = 469.45605 Ave special neighs/atom = 1.6184308 Neighbor list builds = 0 Dangerous builds = 0 undump sci uncompute group_15 unfix group_15 uncompute group_16 unfix group_16 uncompute group_17 unfix group_17 uncompute group_18 unfix group_18 uncompute group_19 unfix group_19 uncompute group_20 unfix group_20 uncompute group_21 unfix group_21 unfix 1 unfix 2 unfix 3 unfix 4 unfix shaken log 2.6_Custom.out