#------------------------------------------------------------------------------- # 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 1 b 1 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 3275 = # 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 sci all custom 1000 2.5.xyz id mol type q xs ys zs compute group_8 subset_Layer2 group/group subset_Li_1 pair yes kspace yes fix group_8 all ave/time 1 100 100 c_group_8 file 2.5_GroupInteractions_Layer2_Li_1_8.out compute group_9 subset_Layer2 group/group subset_K_1 pair yes kspace yes fix group_9 all ave/time 1 100 100 c_group_9 file 2.5_GroupInteractions_Layer2_K_1_9.out compute group_10 subset_Layer2 group/group subset_Mg_1 pair yes kspace yes fix group_10 all ave/time 1 100 100 c_group_10 file 2.5_GroupInteractions_Layer2_Mg_1_10.out compute group_11 subset_Layer2 group/group subset_Cl_1 pair yes kspace yes fix group_11 all ave/time 1 100 100 c_group_11 file 2.5_GroupInteractions_Layer2_Cl_1_11.out compute group_12 subset_Layer2 group/group subset_SO4 pair yes kspace yes fix group_12 all ave/time 1 100 100 c_group_12 file 2.5_GroupInteractions_Layer2_SO4_12.out compute group_13 subset_Layer2 group/group subset_H2O pair yes kspace yes fix group_13 all ave/time 1 100 100 c_group_13 file 2.5_GroupInteractions_Layer2_H2O_13.out timestep 1 run 10000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.2550303 grid = 36 27 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0036863798 estimated relative force accuracy = 1.1101423e-05 using double precision KISS FFT 3d grid and FFT values/proc = 7000 2016 generated 0 of 28 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) 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) 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) 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) 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 = 7 5 15 7 neighbor lists, perpetual/occasional/extra = 1 6 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 SHAKE stats (type/ave/delta/count) on step 0 1 0.97 6.91891e-13 9825 1 103.7 7.61986e-11 3275 Per MPI rank memory allocation (min/avg/max) = 12.97 | 13.31 | 13.65 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 -7264.2677 143340.91 1.3114365 297.04057 44.393748 69.392569 0 0 36933.282 -72546.665 -319.55737 -317415.75 -352915.35 7010.7677 10000 10000 -7094.9282 143340.91 1.3114365 291.14626 31.39117 70.411861 0 0 37242.336 -73151.783 -319.55737 -317422.88 -353230.52 6871.6497 Loop time of 253.485 on 32 procs for 10000 steps with 12250 atoms Performance: 3.408 ns/day, 7.041 hours/ns, 39.450 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 | 42.391 | 52.763 | 61.095 | 70.8 | 20.82 Bond | 0.015411 | 0.035392 | 0.061181 | 7.5 | 0.01 Kspace | 18.448 | 26.848 | 37.287 | 100.4 | 10.59 Neigh | 3.1702 | 3.1782 | 3.1888 | 0.3 | 1.25 Comm | 5.8496 | 6.2996 | 6.6813 | 11.1 | 2.49 Output | 0.011318 | 0.013964 | 0.016569 | 1.3 | 0.01 Modify | 163.67 | 163.97 | 164.3 | 1.8 | 64.69 Other | | 0.3767 | | | 0.15 Nlocal: 382.812 ave 415 max 344 min Histogram: 3 1 4 5 0 5 2 2 6 4 Nghost: 7286.94 ave 7682 max 6833 min Histogram: 4 0 8 0 4 2 2 0 6 6 Neighs: 188235 ave 214966 max 151427 min Histogram: 3 2 3 1 1 5 1 6 7 3 Total # of neighbors = 6023507 Ave neighs/atom = 491.71486 Ave special neighs/atom = 1.6481633 Neighbor list builds = 500 Dangerous builds = 0 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) = 0.2550303 grid = 36 27 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0036863798 estimated relative force accuracy = 1.1101423e-05 using double precision KISS FFT 3d grid and FFT values/proc = 7000 2016 generated 0 of 28 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) 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) 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) 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) 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 10000 1 0.97 1.19927e-06 9825 1 103.7 0.000109765 3275 Per MPI rank memory allocation (min/avg/max) = 17.55 | 19.35 | 20.51 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 -7094.0429 143340.91 1.3114365 291.14626 31.39117 70.411861 0 0 37242.336 -73151.783 -319.55737 -317422.88 -353230.52 6871.6497 Loop time of 7.77603e-06 on 32 procs for 0 steps with 12250 atoms 114.9% 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 | | 7.776e-06 | | |100.00 Nlocal: 382.812 ave 415 max 344 min Histogram: 3 1 4 5 0 5 2 2 6 4 Nghost: 7286.94 ave 7682 max 6833 min Histogram: 4 0 8 0 4 2 2 0 6 6 Neighs: 188235 ave 214966 max 151427 min Histogram: 3 2 3 1 1 5 1 6 7 3 Total # of neighbors = 6023507 Ave neighs/atom = 491.71486 Ave special neighs/atom = 1.6481633 Neighbor list builds = 0 Dangerous builds = 0 undump sci uncompute group_8 unfix group_8 uncompute group_9 unfix group_9 uncompute group_10 unfix group_10 uncompute group_11 unfix group_11 uncompute group_12 unfix group_12 uncompute group_13 unfix group_13 unfix 1 unfix 2 unfix 3 unfix 4 unfix shaken log 2.6_Custom.out