#------------------------------------------------------------------------------- # 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 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 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 sci all custom 300000 2.5.xyz id mol type q xs ys zs compute group_2 subset_Layer2 group/group subset_Layer1 pair yes kspace yes fix group_2 all ave/time 1 100 100 c_group_2 file 2.5_GroupInteractions_Layer2_Layer1_2.out compute group_3 subset_Layer2 group/group subset_Layer1 pair yes kspace no fix group_3 all ave/time 1 100 100 c_group_3 file 2.5_GroupInteractions_Layer2_Layer1_3.out compute group_4 subset_Layer2 group/group subset_Layer1 pair no kspace yes fix group_4 all ave/time 1 100 100 c_group_4 file 2.5_GroupInteractions_Layer2_Layer1_4.out compute group_5 subset_Layer2 group/group subset_Li_1 pair yes kspace yes fix group_5 all ave/time 1 100 100 c_group_5 file 2.5_GroupInteractions_Layer2_Li_1_5.out compute group_6 subset_Layer2 group/group subset_K_1 pair yes kspace yes fix group_6 all ave/time 1 100 100 c_group_6 file 2.5_GroupInteractions_Layer2_K_1_6.out compute group_7 subset_Layer2 group/group subset_Mg_1 pair yes kspace yes fix group_7 all ave/time 1 100 100 c_group_7 file 2.5_GroupInteractions_Layer2_Mg_1_7.out compute group_8 subset_Layer2 group/group subset_Cl_1 pair yes kspace yes fix group_8 all ave/time 1 100 100 c_group_8 file 2.5_GroupInteractions_Layer2_Cl_1_8.out compute group_9 subset_Layer2 group/group subset_SO4 pair yes kspace yes fix group_9 all ave/time 1 100 100 c_group_9 file 2.5_GroupInteractions_Layer2_SO4_9.out compute group_10 subset_Layer2 group/group subset_H2O pair yes kspace yes fix group_10 all ave/time 1 100 100 c_group_10 file 2.5_GroupInteractions_Layer2_H2O_10.out timestep 1 run 3000000 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) 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 9 neighbor lists, perpetual/occasional/extra = 1 8 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 (9) 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 7.48512e-13 9825 1 103.7 7.35412e-11 3275 Per MPI rank memory allocation (min/avg/max) = 12.97 | 13.28 | 13.64 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 -7122.1083 143340.91 1.3114365 294.45612 31.899035 56.934369 0 0 37133.106 -73035.223 -319.55737 -317439.46 -353252.74 6949.7692 SHAKE stats (type/ave/delta/count) on step 50000 1 0.97 1.0318e-06 9825 1 103.7 0.000101403 3275 SHAKE stats (type/ave/delta/count) on step 100000 1 0.97 1.32239e-06 9825 1 103.7 9.9529e-05 3275 SHAKE stats (type/ave/delta/count) on step 150000 1 0.97 1.28335e-06 9825 1 103.7 9.14434e-05 3275 SHAKE stats (type/ave/delta/count) on step 200000 1 0.97 1.37901e-06 9825 1 103.7 9.87751e-05 3275 SHAKE stats (type/ave/delta/count) on step 250000 1 0.97 1.23207e-06 9825 1 103.7 9.36153e-05 3275 SHAKE stats (type/ave/delta/count) on step 300000 1 0.97 1.14098e-06 9825 1 103.7 9.68066e-05 3275 SHAKE stats (type/ave/delta/count) on step 350000 1 0.97 1.28291e-06 9825 1 103.7 9.33906e-05 3275 SHAKE stats (type/ave/delta/count) on step 400000 1 0.97 1.43573e-06 9825 1 103.7 8.51009e-05 3275 SHAKE stats (type/ave/delta/count) on step 450000 1 0.97 1.41938e-06 9825 1 103.7 0.000125316 3275 SHAKE stats (type/ave/delta/count) on step 500000 1 0.97 1.23318e-06 9825 1 103.7 0.000114703 3275 SHAKE stats (type/ave/delta/count) on step 550000 1 0.97 1.46701e-06 9825 1 103.7 0.000111603 3275 SHAKE stats (type/ave/delta/count) on step 600000 1 0.97 1.41377e-06 9825 1 103.7 0.000111899 3275 SHAKE stats (type/ave/delta/count) on step 650000 1 0.97 1.33192e-06 9825 1 103.7 9.77716e-05 3275 SHAKE stats (type/ave/delta/count) on step 700000 1 0.97 1.49694e-06 9825 1 103.7 0.000106658 3275 SHAKE stats (type/ave/delta/count) on step 750000 1 0.97 1.23866e-06 9825 1 103.7 9.94686e-05 3275 SHAKE stats (type/ave/delta/count) on step 800000 1 0.97 1.39554e-06 9825 1 103.7 9.36548e-05 3275 SHAKE stats (type/ave/delta/count) on step 850000 1 0.97 1.25001e-06 9825 1 103.7 9.51205e-05 3275 SHAKE stats (type/ave/delta/count) on step 900000 1 0.97 1.41396e-06 9825 1 103.7 0.000104585 3275 SHAKE stats (type/ave/delta/count) on step 950000 1 0.97 1.342e-06 9825 1 103.7 9.27948e-05 3275 SHAKE stats (type/ave/delta/count) on step 1000000 1 0.97 1.16225e-06 9825 1 103.7 0.000110102 3275 SHAKE stats (type/ave/delta/count) on step 1050000 1 0.97 1.06412e-06 9825 1 103.7 9.32902e-05 3275 SHAKE stats (type/ave/delta/count) on step 1100000 1 0.97 1.21499e-06 9825 1 103.7 0.000106441 3275 SHAKE stats (type/ave/delta/count) on step 1150000 1 0.97 1.11344e-06 9825 1 103.7 0.000105913 3275 SHAKE stats (type/ave/delta/count) on step 1200000 1 0.97 1.17279e-06 9825 1 103.7 0.000100026 3275 SHAKE stats (type/ave/delta/count) on step 1250000 1 0.97 1.83256e-06 9825 1 103.7 0.000128136 3275 SHAKE stats (type/ave/delta/count) on step 1300000 1 0.97 1.13987e-06 9825 1 103.7 9.61613e-05 3275 SHAKE stats (type/ave/delta/count) on step 1350000 1 0.97 1.21198e-06 9825 1 103.7 9.54146e-05 3275 SHAKE stats (type/ave/delta/count) on step 1400000 1 0.97 1.17899e-06 9825 1 103.7 9.15607e-05 3275 SHAKE stats (type/ave/delta/count) on step 1450000 1 0.97 1.23278e-06 9825 1 103.7 9.67713e-05 3275 SHAKE stats (type/ave/delta/count) on step 1500000 1 0.97 1.65354e-06 9825 1 103.7 0.000105866 3275 SHAKE stats (type/ave/delta/count) on step 1550000 1 0.97 1.40643e-06 9825 1 103.7 0.000102932 3275 SHAKE stats (type/ave/delta/count) on step 1600000 1 0.97 1.23771e-06 9825 1 103.7 9.32637e-05 3275 SHAKE stats (type/ave/delta/count) on step 1650000 1 0.97 1.41465e-06 9825 1 103.7 9.87561e-05 3275 SHAKE stats (type/ave/delta/count) on step 1700000 1 0.97 1.34987e-06 9825 1 103.7 0.000109061 3275 SHAKE stats (type/ave/delta/count) on step 1750000 1 0.97 1.21578e-06 9825 1 103.7 9.27085e-05 3275 SHAKE stats (type/ave/delta/count) on step 1800000 1 0.97 1.2332e-06 9825 1 103.7 9.0217e-05 3275 SHAKE stats (type/ave/delta/count) on step 1850000 1 0.97 1.33503e-06 9825 1 103.7 9.0259e-05 3275 SHAKE stats (type/ave/delta/count) on step 1900000 1 0.97 1.18728e-06 9825 1 103.7 9.30264e-05 3275 SHAKE stats (type/ave/delta/count) on step 1950000 1 0.97 1.11001e-06 9825 1 103.7 9.10274e-05 3275 SHAKE stats (type/ave/delta/count) on step 2000000 1 0.97 1.40277e-06 9825 1 103.7 0.000112373 3275 SHAKE stats (type/ave/delta/count) on step 2050000 1 0.97 1.70283e-06 9825 1 103.7 0.000103056 3275 SHAKE stats (type/ave/delta/count) on step 2100000 1 0.97 1.09272e-06 9825 1 103.7 0.000104043 3275 SHAKE stats (type/ave/delta/count) on step 2150000 1 0.97 1.18503e-06 9825 1 103.7 9.98184e-05 3275 SHAKE stats (type/ave/delta/count) on step 2200000 1 0.97 1.65599e-06 9825 1 103.7 9.50883e-05 3275 SHAKE stats (type/ave/delta/count) on step 2250000 1 0.97 1.24826e-06 9825 1 103.7 9.88847e-05 3275 SHAKE stats (type/ave/delta/count) on step 2300000 1 0.97 1.73502e-06 9825 1 103.7 0.000116961 3275 SHAKE stats (type/ave/delta/count) on step 2350000 1 0.97 1.17473e-06 9825 1 103.7 9.45421e-05 3275 SHAKE stats (type/ave/delta/count) on step 2400000 1 0.97 1.17204e-06 9825 1 103.7 9.81206e-05 3275 SHAKE stats (type/ave/delta/count) on step 2450000 1 0.97 1.08189e-06 9825 1 103.7 9.50778e-05 3275 SHAKE stats (type/ave/delta/count) on step 2500000 1 0.97 1.1867e-06 9825 1 103.7 9.61434e-05 3275 SHAKE stats (type/ave/delta/count) on step 2550000 1 0.97 1.41958e-06 9825 1 103.7 0.000117769 3275 SHAKE stats (type/ave/delta/count) on step 2600000 1 0.97 1.42752e-06 9825 1 103.7 0.00011633 3275 SHAKE stats (type/ave/delta/count) on step 2650000 1 0.97 1.08294e-06 9825 1 103.7 8.80452e-05 3275 SHAKE stats (type/ave/delta/count) on step 2700000 1 0.97 1.17098e-06 9825 1 103.7 9.61589e-05 3275 SHAKE stats (type/ave/delta/count) on step 2750000 1 0.97 1.04195e-06 9825 1 103.7 8.92298e-05 3275 SHAKE stats (type/ave/delta/count) on step 2800000 1 0.97 1.28909e-06 9825 1 103.7 9.25705e-05 3275 SHAKE stats (type/ave/delta/count) on step 2850000 1 0.97 1.1811e-06 9825 1 103.7 0.0001033 3275 SHAKE stats (type/ave/delta/count) on step 2900000 1 0.97 1.06149e-06 9825 1 103.7 9.1423e-05 3275 SHAKE stats (type/ave/delta/count) on step 2950000 1 0.97 1.20664e-06 9825 1 103.7 9.78578e-05 3275 SHAKE stats (type/ave/delta/count) on step 3000000 1 0.97 1.30461e-06 9825 1 103.7 9.17378e-05 3275 3000000 3000000 -7267.778 143340.91 1.3114365 300.91064 35.404094 60.857251 0 0 36957.845 -73067.711 -319.55737 -317439.9 -353453.51 7102.1091 Loop time of 100671 on 32 procs for 3000000 steps with 12250 atoms Performance: 2.575 ns/day, 9.321 hours/ns, 29.800 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 | 12699 | 15588 | 17361 |1091.8 | 15.48 Bond | 4.2861 | 9.59 | 18.26 | 120.7 | 0.01 Kspace | 5919 | 7716.2 | 10627 |1570.7 | 7.66 Neigh | 931.17 | 934.54 | 938.13 | 8.1 | 0.93 Comm | 1802 | 1905.9 | 1971.9 | 129.1 | 1.89 Output | 0.011544 | 0.014283 | 0.016969 | 1.4 | 0.00 Modify | 74334 | 74383 | 74454 | 14.7 | 73.89 Other | | 133.8 | | | 0.13 Nlocal: 382.812 ave 411 max 340 min Histogram: 1 2 1 3 4 1 6 7 6 1 Nghost: 7265.28 ave 7565 max 6952 min Histogram: 5 3 4 1 3 1 3 1 6 5 Neighs: 188113 ave 209735 max 150175 min Histogram: 2 2 2 2 0 1 5 6 10 2 Total # of neighbors = 6019611 Ave neighs/atom = 491.39682 Ave special neighs/atom = 1.6481633 Neighbor list builds = 149532 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) = 0.2550303 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) 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 3000000 1 0.97 1.30461e-06 9825 1 103.7 9.17378e-05 3275 Per MPI rank memory allocation (min/avg/max) = 19.07 | 21.84 | 22.8 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 -7266.9964 143340.91 1.3114365 300.91064 35.404094 60.857251 0 0 36957.845 -73067.711 -319.55737 -317439.9 -353453.51 7102.1091 Loop time of 1.06836e-05 on 32 procs for 0 steps with 12250 atoms 111.4% 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 | | 1.068e-05 | | |100.00 Nlocal: 382.812 ave 411 max 340 min Histogram: 1 2 1 3 4 1 6 7 6 1 Nghost: 7265.28 ave 7565 max 6952 min Histogram: 5 3 4 1 3 1 3 1 6 5 Neighs: 188113 ave 209735 max 150175 min Histogram: 2 2 2 2 0 1 5 6 10 2 Total # of neighbors = 6019611 Ave neighs/atom = 491.39682 Ave special neighs/atom = 1.6481633 Neighbor list builds = 0 Dangerous builds = 0 undump sci uncompute group_2 unfix group_2 uncompute group_3 unfix group_3 uncompute group_4 unfix group_4 uncompute group_5 unfix group_5 uncompute group_6 unfix group_6 uncompute group_7 unfix group_7 uncompute group_8 unfix group_8 uncompute group_9 unfix group_9 uncompute group_10 unfix group_10 unfix 1 unfix 2 unfix 3 unfix 4 unfix shaken Total wall time: 30:34:19