#------------------------------------------------------------------------------- # 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 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 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_22 subset_Layer2 group/group subset_Li_1 pair yes kspace no fix group_22 all ave/time 1 100 100 c_group_22 file 2.5_GroupInteractions_Layer2_Li_1_22.out compute group_23 subset_Layer2 group/group subset_Na_1 pair yes kspace no fix group_23 all ave/time 1 100 100 c_group_23 file 2.5_GroupInteractions_Layer2_Na_1_23.out compute group_24 subset_Layer2 group/group subset_K_1 pair yes kspace no fix group_24 all ave/time 1 100 100 c_group_24 file 2.5_GroupInteractions_Layer2_K_1_24.out compute group_25 subset_Layer2 group/group subset_Mg_1 pair yes kspace no fix group_25 all ave/time 1 100 100 c_group_25 file 2.5_GroupInteractions_Layer2_Mg_1_25.out compute group_26 subset_Layer2 group/group subset_Cl_1 pair yes kspace no fix group_26 all ave/time 1 100 100 c_group_26 file 2.5_GroupInteractions_Layer2_Cl_1_26.out compute group_27 subset_Layer2 group/group subset_SO4 pair yes kspace no fix group_27 all ave/time 1 100 100 c_group_27 file 2.5_GroupInteractions_Layer2_SO4_27.out compute group_28 subset_Layer2 group/group subset_H2O pair yes kspace no fix group_28 all ave/time 1 100 100 c_group_28 file 2.5_GroupInteractions_Layer2_H2O_28.out timestep 1 run 3000000 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 = 11132 3600 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 7.66054e-13 8436 2 103.7 9.08074e-11 2812 Per MPI rank memory allocation (min/avg/max) = 12.83 | 14.11 | 14.79 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 -288.28357 141184.09 1.4079299 296.82941 48.771212 66.923035 0 0 31887.79 -35591.404 -312.04795 -284074.92 -287662.84 6787.2401 SHAKE stats (type/ave/delta/count) on step 50000 2 0.97 1.18102e-06 8436 2 103.7 9.29175e-05 2812 SHAKE stats (type/ave/delta/count) on step 100000 2 0.97 1.17038e-06 8436 2 103.7 9.95441e-05 2812 SHAKE stats (type/ave/delta/count) on step 150000 2 0.97 1.76481e-06 8436 2 103.7 0.000119135 2812 SHAKE stats (type/ave/delta/count) on step 200000 2 0.97 1.21306e-06 8436 2 103.7 9.3281e-05 2812 SHAKE stats (type/ave/delta/count) on step 250000 2 0.97 1.43793e-06 8436 2 103.7 0.000107101 2812 SHAKE stats (type/ave/delta/count) on step 300000 2 0.97 1.20457e-06 8436 2 103.7 9.3861e-05 2812 SHAKE stats (type/ave/delta/count) on step 350000 2 0.97 1.60359e-06 8436 2 103.7 9.41919e-05 2812 SHAKE stats (type/ave/delta/count) on step 400000 2 0.97 1.23305e-06 8436 2 103.7 0.000119356 2812 SHAKE stats (type/ave/delta/count) on step 450000 2 0.97 1.08046e-06 8436 2 103.7 0.000102476 2812 SHAKE stats (type/ave/delta/count) on step 500000 2 0.97 1.32042e-06 8436 2 103.7 8.90173e-05 2812 SHAKE stats (type/ave/delta/count) on step 550000 2 0.97 1.09951e-06 8436 2 103.7 9.6008e-05 2812 SHAKE stats (type/ave/delta/count) on step 600000 2 0.97 1.20004e-06 8436 2 103.7 0.000102289 2812 SHAKE stats (type/ave/delta/count) on step 650000 2 0.97 1.43708e-06 8436 2 103.7 0.000101209 2812 SHAKE stats (type/ave/delta/count) on step 700000 2 0.97 1.27995e-06 8436 2 103.7 9.98778e-05 2812 SHAKE stats (type/ave/delta/count) on step 750000 2 0.97 1.23568e-06 8436 2 103.7 0.00010291 2812 SHAKE stats (type/ave/delta/count) on step 800000 2 0.97 1.26295e-06 8436 2 103.7 9.36333e-05 2812 SHAKE stats (type/ave/delta/count) on step 850000 2 0.97 1.01108e-06 8436 2 103.7 9.37655e-05 2812 SHAKE stats (type/ave/delta/count) on step 900000 2 0.97 1.15832e-06 8436 2 103.7 9.68185e-05 2812 SHAKE stats (type/ave/delta/count) on step 950000 2 0.97 1.2299e-06 8436 2 103.7 9.44549e-05 2812 SHAKE stats (type/ave/delta/count) on step 1000000 2 0.97 1.1352e-06 8436 2 103.7 0.000101631 2812 SHAKE stats (type/ave/delta/count) on step 1050000 2 0.97 1.29995e-06 8436 2 103.7 9.54353e-05 2812 SHAKE stats (type/ave/delta/count) on step 1100000 2 0.97 1.31052e-06 8436 2 103.7 9.2283e-05 2812 SHAKE stats (type/ave/delta/count) on step 1150000 2 0.97 1.25602e-06 8436 2 103.7 9.0299e-05 2812 SHAKE stats (type/ave/delta/count) on step 1200000 2 0.97 1.13743e-06 8436 2 103.7 0.000100268 2812 SHAKE stats (type/ave/delta/count) on step 1250000 2 0.97 1.20049e-06 8436 2 103.7 0.000110637 2812 SHAKE stats (type/ave/delta/count) on step 1300000 2 0.97 1.17169e-06 8436 2 103.7 0.000109731 2812 SHAKE stats (type/ave/delta/count) on step 1350000 2 0.97 1.43974e-06 8436 2 103.7 0.00010403 2812 SHAKE stats (type/ave/delta/count) on step 1400000 2 0.97 1.32598e-06 8436 2 103.7 0.000107982 2812 SHAKE stats (type/ave/delta/count) on step 1450000 2 0.97 1.44865e-06 8436 2 103.7 0.000108246 2812 SHAKE stats (type/ave/delta/count) on step 1500000 2 0.97 1.30919e-06 8436 2 103.7 9.81938e-05 2812 SHAKE stats (type/ave/delta/count) on step 1550000 2 0.97 1.1778e-06 8436 2 103.7 9.57145e-05 2812 SHAKE stats (type/ave/delta/count) on step 1600000 2 0.97 1.37147e-06 8436 2 103.7 9.2492e-05 2812 SHAKE stats (type/ave/delta/count) on step 1650000 2 0.97 1.24882e-06 8436 2 103.7 9.03007e-05 2812 SHAKE stats (type/ave/delta/count) on step 1700000 2 0.97 1.26202e-06 8436 2 103.7 0.00010317 2812 SHAKE stats (type/ave/delta/count) on step 1750000 2 0.97 1.11582e-06 8436 2 103.7 9.6855e-05 2812 SHAKE stats (type/ave/delta/count) on step 1800000 2 0.97 1.25195e-06 8436 2 103.7 0.000103559 2812 SHAKE stats (type/ave/delta/count) on step 1850000 2 0.97 1.20064e-06 8436 2 103.7 0.000104703 2812 SHAKE stats (type/ave/delta/count) on step 1900000 2 0.97 1.12306e-06 8436 2 103.7 9.89392e-05 2812 SHAKE stats (type/ave/delta/count) on step 1950000 2 0.97 1.24348e-06 8436 2 103.7 0.000106659 2812 SHAKE stats (type/ave/delta/count) on step 2000000 2 0.97 1.09675e-06 8436 2 103.7 0.000100463 2812 SHAKE stats (type/ave/delta/count) on step 2050000 2 0.97 1.45652e-06 8436 2 103.7 0.000132943 2812 SHAKE stats (type/ave/delta/count) on step 2100000 2 0.97 1.28446e-06 8436 2 103.7 9.52236e-05 2812 SHAKE stats (type/ave/delta/count) on step 2150000 2 0.97 1.20613e-06 8436 2 103.7 9.88664e-05 2812 SHAKE stats (type/ave/delta/count) on step 2200000 2 0.97 1.43802e-06 8436 2 103.7 0.000112197 2812 SHAKE stats (type/ave/delta/count) on step 2250000 2 0.97 1.1615e-06 8436 2 103.7 0.000107282 2812 SHAKE stats (type/ave/delta/count) on step 2300000 2 0.97 1.21758e-06 8436 2 103.7 8.90857e-05 2812 SHAKE stats (type/ave/delta/count) on step 2350000 2 0.97 1.10035e-06 8436 2 103.7 9.87187e-05 2812 SHAKE stats (type/ave/delta/count) on step 2400000 2 0.97 1.17849e-06 8436 2 103.7 9.24139e-05 2812 SHAKE stats (type/ave/delta/count) on step 2450000 2 0.97 1.5936e-06 8436 2 103.7 0.000108707 2812 SHAKE stats (type/ave/delta/count) on step 2500000 2 0.97 1.11718e-06 8436 2 103.7 9.25926e-05 2812 SHAKE stats (type/ave/delta/count) on step 2550000 2 0.97 1.19962e-06 8436 2 103.7 9.94895e-05 2812 SHAKE stats (type/ave/delta/count) on step 2600000 2 0.97 1.20401e-06 8436 2 103.7 9.49562e-05 2812 SHAKE stats (type/ave/delta/count) on step 2650000 2 0.97 1.07745e-06 8436 2 103.7 9.02236e-05 2812 SHAKE stats (type/ave/delta/count) on step 2700000 2 0.97 1.29337e-06 8436 2 103.7 9.31487e-05 2812 SHAKE stats (type/ave/delta/count) on step 2750000 2 0.97 1.17831e-06 8436 2 103.7 9.60287e-05 2812 SHAKE stats (type/ave/delta/count) on step 2800000 2 0.97 1.13488e-06 8436 2 103.7 0.000100651 2812 SHAKE stats (type/ave/delta/count) on step 2850000 2 0.97 1.19976e-06 8436 2 103.7 9.89819e-05 2812 SHAKE stats (type/ave/delta/count) on step 2900000 2 0.97 1.08549e-06 8436 2 103.7 9.28414e-05 2812 SHAKE stats (type/ave/delta/count) on step 2950000 2 0.97 1.17075e-06 8436 2 103.7 9.7249e-05 2812 SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.40342e-06 8436 2 103.7 9.30541e-05 2812 3000000 3000000 -592.25081 141184.09 1.4079299 295.48768 41.45347 73.379239 0 0 31732.942 -35392.391 -312.04795 -284064.54 -287609.16 6756.5604 Loop time of 49064.1 on 16 procs for 3000000 steps with 10808 atoms Performance: 5.283 ns/day, 4.543 hours/ns, 61.145 timesteps/s 98.8% CPU use with 16 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5913.5 | 21573 | 30142 |6106.0 | 43.97 Bond | 3.6946 | 10.373 | 21.726 | 153.0 | 0.02 Kspace | 5627 | 14216 | 29895 |7532.7 | 28.97 Neigh | 1564.8 | 1568.1 | 1572.2 | 6.2 | 3.20 Comm | 749.76 | 887.79 | 961.9 | 266.2 | 1.81 Output | 0.014298 | 0.016207 | 0.018014 | 0.9 | 0.00 Modify | 10690 | 10744 | 10857 | 62.7 | 21.90 Other | | 64.71 | | | 0.13 Nlocal: 675.5 ave 802 max 348 min Histogram: 4 0 0 0 0 0 0 0 1 11 Nghost: 8230.81 ave 9785 max 7109 min Histogram: 4 0 2 5 1 0 0 0 0 4 Neighs: 316427 ave 420478 max 87182 min Histogram: 4 0 0 0 0 0 0 1 3 8 Total # of neighbors = 5062829 Ave neighs/atom = 468.43348 Ave special neighs/atom = 1.6184308 Neighbor list builds = 149335 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) = 0.25537807 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 = 11132 3600 generated 0 of 36 mixed pair_coeff terms from sixthpower mixing rule SHAKE stats (type/ave/delta/count) on step 3000000 2 0.97 1.40342e-06 8436 2 103.7 9.30541e-05 2812 Per MPI rank memory allocation (min/avg/max) = 15.5 | 24.57 | 28.14 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 -591.68444 141184.09 1.4079299 295.48768 41.45347 73.379239 0 0 31732.942 -35392.391 -312.04795 -284064.54 -287609.16 6756.5604 Loop time of 3.80962e-06 on 16 procs for 0 steps with 10808 atoms 139.4% CPU use with 16 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 | | 3.81e-06 | | |100.00 Nlocal: 675.5 ave 802 max 348 min Histogram: 4 0 0 0 0 0 0 0 1 11 Nghost: 8230.81 ave 9785 max 7109 min Histogram: 4 0 2 5 1 0 0 0 0 4 Neighs: 316427 ave 420478 max 87182 min Histogram: 4 0 0 0 0 0 0 1 3 8 Total # of neighbors = 5062829 Ave neighs/atom = 468.43348 Ave special neighs/atom = 1.6184308 Neighbor list builds = 0 Dangerous builds = 0 undump sci uncompute group_22 unfix group_22 uncompute group_23 unfix group_23 uncompute group_24 unfix group_24 uncompute group_25 unfix group_25 uncompute group_26 unfix group_26 uncompute group_27 unfix group_27 uncompute group_28 unfix group_28 unfix 1 unfix 2 unfix 3 unfix 4 unfix shaken Total wall time: 17:26:10