LAMMPS (7 Jan 2022) using 1 OpenMP thread(s) per MPI task log 2.1_Initialize.out #------------------------------------------------------------------------------- # Stage 2.1: Initialize LAMMPS run for 3-d periodic #------------------------------------------------------------------------------- units real boundary p p p atom_style full pair_style lj/class2/coul/long 9.5 pair_modify mix sixthpower pair_modify tail yes bond_style class2 angle_style class2 dihedral_style class2 improper_style class2 special_bonds lj 0.0 0.0 1.0 coul 0.0 0.0 1.0 box tilt large read_data structure.dat Reading data file ... triclinic box = (0 0 0) to (9.975 7.186 23.982633) with tilt (0 -3.704136 0) 1 by 1 by 2 MPI processor grid reading atoms ... 192 atoms scanning bonds ... 1 = max bonds/atom scanning angles ... 6 = max angles/atom scanning impropers ... 4 = max impropers/atom reading bonds ... 128 bonds reading angles ... 96 angles reading impropers ... 32 impropers Finding 1-2 1-3 1-4 neighbors ... special bond factors lj: 0 0 1 special bond factors coul: 0 0 1 4 = max # of 1-2 neighbors 3 = max # of 1-3 neighbors 4 = max # of special neighbors special bonds CPU = 0.000 seconds read_data CPU = 0.008 seconds include parameters.dat bond_coeff 1 0.97 563.28 -1428.2 1902.1 # h* o* bond_coeff 2 1.5325 277.56 -433.25 2922.8 # o1S- s4o- angle_coeff 1 109.47 87.637 -98.528 174.89 # o1S- s4o- o1S- angle_coeff 2 103.7 49.84 -11.6 -8 # h* o* h* dihedral_coeff 1 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 # xxx xxx xxx xxx improper_coeff 1 0 0 # * s_ * * angle_coeff 1 bb 130.45 1.5325 1.5325 # o1S- s4o- o1S- angle_coeff 2 bb -9.5 0.97 0.97 # h* o* h* angle_coeff 1 ba 0.0 0.0 1.5325 1.5325 # o1S- s4o- o1S- angle_coeff 2 ba 22.35 22.35 0.97 0.97 # h* o* h* dihedral_coeff 1 mbt 0.0000 0.0000 0.0000 0.0 # xxx xxx xxx xxx dihedral_coeff 1 ebt 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0 0.0 # xxx xxx xxx xxx dihedral_coeff 1 at 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0 0.0 # xxx xxx xxx xxx dihedral_coeff 1 aat 0.0000 0.0 0.0 # xxx xxx xxx xxx dihedral_coeff 1 bb13 0.0 0.0 0.0 # xxx xxx xxx xxx improper_coeff 1 aa 0.0 0.0 0.0 120.0 120.0 120.0 # * s_ * * pair_coeff 1 1 0 1.098 # hw - pair_coeff 2 2 0.2951 2.3959 # mg+ - pair_coeff 3 3 0.148 3.7824 # o* - pair_coeff 4 4 0.1436 3.6173 # o1S- - pair_coeff 5 5 0.24 4.08 # s4o- - neighbor 2.0 bin neigh_modify delay 0 every 1 check yes kspace_style pppm 0.00001 variable R equal 0.00198722 variable sysvol equal vol variable sysmass equal mass(all)/6.0221367e+23 variable sysdensity equal v_sysmass/v_sysvol/1.0e-24 variable coulomb equal ecoul+elong variable etotal equal etotal variable pe equal pe variable ke equal ke variable evdwl equal evdwl variable epair equal epair variable ebond equal ebond variable eangle equal eangle variable edihed equal edihed variable eimp equal eimp variable lx equal lx variable ly equal ly variable lz equal lz variable Nthermo equal 0 variable cella equal lx variable cellb equal sqrt(ly*ly+xy*xy) variable cellc equal sqrt(lz*lz+xz*xz+yz*yz) variable cellalpha equal acos((xy*xz+ly*yz)/(v_cellb*v_cellc)) variable cellbeta equal acos(xz/v_cellc) variable cellgamma equal acos(xy/v_cellb) variable p equal press variable pxx equal pxx variable pyy equal pyy variable pzz equal pzz variable pyz equal pyz variable pxz equal pxz variable pxy equal pxy variable sxx equal -pxx variable syy equal -pyy variable szz equal -pzz variable syz equal -pyz variable sxz equal -pxz variable sxy equal -pxy variable fmax equal fmax variable fnorm equal fnorm variable time equal step*dt+0.000001 variable surfacetension equal 0.5*v_lz*(0.5*(v_sxx+v_syy)-v_szz) thermo_style custom step v_time press vol v_sysdensity temp ebond eangle edihed eimp evdwl ecoul etail elong pe ke thermo_modify flush yes # # Set up the fixed and movable groups # group movable union all 192 atoms in group movable group fixed subtract all movable 0 atoms in group fixed compute sum_f1 movable reduce sum fx fy fz variable sum_fx equal c_sum_f1[1] variable sum_fy equal c_sum_f1[2] variable sum_fz equal c_sum_f1[3] log 2.2_Minimization.out #------------------------------------------------------------------------------- # Stage 2.2: Minimization #------------------------------------------------------------------------------- min_style cg min_modify dmax 0.05 line fast reset_timestep 0 thermo_style custom step fmax fnorm press vol v_sysdensity v_sxx v_syy v_szz v_syz v_sxz v_sxy pe v_cella v_cellb v_cellc v_cellalpha v_cellbeta v_cellgamma v_sum_fx v_sum_fy v_sum_fz WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:888) dump sci all custom 1000 2.2.xyz id mol type q xs ys zs thermo 100 minimize 0.0 1.0 1000 10000 PPPM initialization ... WARNING: System is not charge neutral, net charge = 0.0008 (../kspace.cpp:325) using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.34435248 grid = 12 12 27 stencil order = 5 estimated absolute RMS force accuracy = 0.0015842633 estimated relative force accuracy = 4.7709617e-06 using double precision KISS FFT 3d grid and FFT values/proc = 8379 2016 generated 0 of 10 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 = 11.5 ghost atom cutoff = 11.5 binsize = 5.75, bins = 3 2 5 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair lj/class2/coul/long, perpetual attributes: half, newton on pair build: half/bin/newton/tri stencil: half/bin/3d/tri bin: standard Setting up cg style minimization ... Unit style : real Current step : 0 Per MPI rank memory allocation (min/avg/max) = 12.67 | 12.67 | 12.67 Mbytes Step Fmax Fnorm Press Volume v_sysdensity v_sxx v_syy v_szz v_syz v_sxz v_sxy PotEng v_cella v_cellb v_cellc v_cellalpha v_cellbeta v_cellgamma v_sum_fx v_sum_fy v_sum_fz 0 78.432622 725.6942 -43897.957 1719.0835 1.7654279 44176.715 66628.248 20888.908 -0.047342945 33132.86 0.26193689 -5870.5308 9.975 7.186 24.267 1.5707963 1.7240362 1.5707963 -1.438849e-13 2.1316282e-14 -3.9497919e-13 100 0.250149 1.8749095 -24047.117 1719.0835 1.7654279 21534.271 38151.554 12455.527 3.1834686 108.665 2.9139972 -6480.4952 9.975 7.186 24.267 1.5707963 1.7240362 1.5707963 6.4330485e-14 -1.89182e-13 9.5312647e-14 127 0.11044269 0.95657463 -23954.896 1719.0835 1.7654279 21459.919 37694.814 12709.955 1.5878746 256.57392 1.9700467 -6480.5094 9.975 7.186 24.267 1.5707963 1.7240362 1.5707963 3.5916409e-13 2.0075608e-13 -2.5264513e-13 Loop time of 0.357467 on 2 procs for 127 steps with 192 atoms 99.5% CPU use with 2 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = force tolerance Energy initial, next-to-last, final = -5870.53076385731 -6480.50818720901 -6480.5094144827 Force two-norm initial, final = 725.6942 0.95657463 Force max component initial, final = 78.432622 0.11044269 Final line search alpha, max atom move = 0.0013832969 0.00015277503 Iterations, force evaluations = 127 241 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.19657 | 0.19726 | 0.19795 | 0.2 | 55.18 Bond | 0.0013703 | 0.0013736 | 0.0013769 | 0.0 | 0.38 Kspace | 0.13976 | 0.14046 | 0.14116 | 0.2 | 39.29 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.015413 | 0.015456 | 0.015499 | 0.0 | 4.32 Output | 8.3405e-05 | 8.7238e-05 | 9.1071e-05 | 0.0 | 0.02 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002832 | | | 0.79 Nlocal: 96 ave 97 max 95 min Histogram: 1 0 0 0 0 0 0 0 0 1 Nghost: 3863 ave 3864 max 3862 min Histogram: 1 0 0 0 0 0 0 0 0 1 Neighs: 34024 ave 34379 max 33669 min Histogram: 1 0 0 0 0 0 0 0 0 1 Total # of neighbors = 68048 Ave neighs/atom = 354.41667 Ave special neighs/atom = 2.3333333 Neighbor list builds = 0 Dangerous builds = 0 undump sci log 2.3_Minimization.out #------------------------------------------------------------------------------- # Stage 2.3: Minimization #------------------------------------------------------------------------------- min_style cg min_modify dmax 0.05 line fast reset_timestep 0 thermo_style custom step fmax fnorm press vol v_sysdensity v_sxx v_syy v_szz v_syz v_sxz v_sxy pe v_cella v_cellb v_cellc v_cellalpha v_cellbeta v_cellgamma v_sum_fx v_sum_fy v_sum_fz fix 2_3_1 all box/relax x 0.987 y 0.987 z 0.987 couple none vmax 0.01 dilate all dump sci all custom 1000 2.3.xyz id mol type q xs ys zs thermo 100 minimize 0.0 1.0 1000 10000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.34435248 grid = 12 12 27 stencil order = 5 estimated absolute RMS force accuracy = 0.0015842633 estimated relative force accuracy = 4.7709617e-06 using double precision KISS FFT 3d grid and FFT values/proc = 8379 2016 generated 0 of 10 mixed pair_coeff terms from sixthpower mixing rule Setting up cg style minimization ... Unit style : real Current step : 0 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 12.67 | 12.67 | 12.67 Mbytes Step Fmax Fnorm Press Volume v_sysdensity v_sxx v_syy v_szz v_syz v_sxz v_sxy PotEng v_cella v_cellb v_cellc v_cellalpha v_cellbeta v_cellgamma v_sum_fx v_sum_fy v_sum_fz 0 0.11044269 0.95657463 -23954.896 1719.0835 1.7654279 21459.919 37694.814 12709.955 1.5878746 256.57392 1.9700467 -6480.5094 9.975 7.186 24.267 1.5707963 1.7240362 1.5707963 3.8461595e-13 1.4016566e-13 -6.1679828e-14 100 3.7919188 17.97865 -33.156163 1599.2777 1.8976805 -462.47628 635.61107 -73.666294 -26.178225 332.51552 -42.233895 -6525.432 9.7761111 6.5918632 25.111277 1.5707963 1.7240362 1.5707963 1.7938429e-13 -1.8651747e-14 -2.304823e-13 200 0.52115928 3.2632116 56.543175 1601.8614 1.8946196 228.64998 -124.12849 -274.15102 -1.3019624 583.46568 11.85538 -6527.414 9.8013963 6.542369 25.276748 1.5707963 1.7240362 1.5707963 1.4099832e-13 -3.7581049e-14 -2.5517088e-13 300 1.7710631 9.486404 35.934592 1600.6248 1.8960833 -234.55559 351.18186 -224.43005 -38.767589 -2194.6051 19.310804 -6529.3161 9.724017 6.4849649 25.683574 1.5707963 1.7240362 1.5707963 2.6587066e-13 -7.860379e-14 3.1008529e-13 400 0.39855447 2.2125886 0.59949055 1599.6381 1.8972529 -50.623971 -33.608179 82.433678 -36.80039 -2340.0783 10.902766 -6529.9553 9.7229418 6.4777317 25.699244 1.5707963 1.7240362 1.5707963 1.3708479e-13 -1.1612933e-13 3.0836445e-13 500 0.13372823 0.84480839 -5.1110293 1599.759 1.8971095 19.689376 18.56041 -22.916698 3.2194762 -2374.4112 -2.5648479 -6529.9822 9.7218421 6.4810481 25.690939 1.5707963 1.7240362 1.5707963 1.3066631e-13 -3.9401815e-13 2.6588454e-13 505 0.098687102 0.63540835 13.338283 1599.7217 1.8971538 6.0944144 -15.901067 -30.208196 3.3343276 -2357.2937 -3.4560667 -6529.9826 9.7220836 6.4810116 25.689847 1.5707963 1.7240362 1.5707963 -1.062761e-13 -4.1389114e-13 2.7348956e-13 WARNING: Bond/angle/dihedral extent > half of periodic box length (../domain.cpp:935) Loop time of 2.21183 on 2 procs for 505 steps with 192 atoms 99.5% CPU use with 2 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = force tolerance Energy initial, next-to-last, final = -6480.5094144827 -6529.9844699835 -6529.98433556928 Force two-norm initial, final = 1133.2327 0.99801257 Force max component initial, final = 945.07406 0.64398075 Final line search alpha, max atom move = 1.8166539e-05 1.1698901e-05 Iterations, force evaluations = 505 1052 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.89736 | 0.90059 | 0.90382 | 0.3 | 40.72 Bond | 0.0063865 | 0.006427 | 0.0064676 | 0.1 | 0.29 Kspace | 0.5909 | 0.59434 | 0.59779 | 0.4 | 26.87 Neigh | 0.002378 | 0.0023795 | 0.002381 | 0.0 | 0.11 Comm | 0.070016 | 0.070494 | 0.070971 | 0.2 | 3.19 Output | 0.00045683 | 0.00047353 | 0.00049024 | 0.0 | 0.02 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.6371 | | | 28.81 Nlocal: 96 ave 98 max 94 min Histogram: 1 0 0 0 0 0 0 0 0 1 Nghost: 4167 ave 4169 max 4165 min Histogram: 1 0 0 0 0 0 0 0 0 1 Neighs: 36488 ave 37256 max 35720 min Histogram: 1 0 0 0 0 0 0 0 0 1 Total # of neighbors = 72976 Ave neighs/atom = 380.08333 Ave special neighs/atom = 2.3333333 Neighbor list builds = 2 Dangerous builds = 0 undump sci unfix 2_3_1 Total wall time: 0:00:02