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 (9.89371 25.149094 23.1) with tilt (-4.666103 0 0) 1 by 2 by 1 MPI processor grid reading atoms ... 288 atoms scanning bonds ... 1 = max bonds/atom scanning angles ... 6 = max angles/atom scanning impropers ... 4 = max impropers/atom reading bonds ... 192 bonds reading angles ... 144 angles reading impropers ... 48 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 = 0.009 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 288 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 = 0.0012 (../kspace.cpp:325) using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.34129482 grid = 15 30 24 stencil order = 5 estimated absolute RMS force accuracy = 0.0012805345 estimated relative force accuracy = 3.8562915e-06 using double precision KISS FFT 3d grid and FFT values/proc = 16368 5400 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 5 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) = 13.24 | 13.24 | 13.25 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 0 245.35851 2028.2289 -113258.63 5747.6922 0.79203564 125455.93 98170.655 116149.3 -3337.379 124.48696 553.79929 -7353.8593 9.89371 25.5783 23.1 1.5707963 1.5707963 1.7542479 2.8421709e-14 -1.1368684e-13 -5.6843419e-13 100 2.1768906 15.750177 -3215.9262 5747.6922 0.79203564 7817.6807 1398.7284 431.36952 385.32788 24.359098 -1270.5778 -9519.2128 9.89371 25.5783 23.1 1.5707963 1.5707963 1.7542479 -7.4606987e-14 2.3503421e-13 -1.9628743e-13 200 0.34122004 1.5049673 -2746.4662 5747.6922 0.79203564 7484.428 506.57359 248.39709 10.092864 -8.6064073 -1897.867 -9528.4156 9.89371 25.5783 23.1 1.5707963 1.5707963 1.7542479 5.714873e-14 -4.6926352e-13 8.1823437e-14 204 0.14324413 0.95233729 -2740.1345 5747.6922 0.79203564 7481.7962 505.7845 232.82285 0.069355098 -3.6737695 -1887.4498 -9528.4216 9.89371 25.5783 23.1 1.5707963 1.5707963 1.7542479 -2.0197732e-13 -4.948264e-13 -1.9201307e-13 Loop time of 0.817119 on 2 procs for 204 steps with 288 atoms 99.7% CPU use with 2 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = force tolerance Energy initial, next-to-last, final = -7353.85930250256 -9528.42063399727 -9528.42155139148 Force two-norm initial, final = 2028.2289 0.95233729 Force max component initial, final = 245.35851 0.14324413 Final line search alpha, max atom move = 0.0014291446 0.00020471656 Iterations, force evaluations = 204 380 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.2969 | 0.30031 | 0.30372 | 0.6 | 36.75 Bond | 0.0030591 | 0.0030635 | 0.0030678 | 0.0 | 0.37 Kspace | 0.48917 | 0.49254 | 0.4959 | 0.5 | 60.28 Neigh | 0.0043901 | 0.0043983 | 0.0044065 | 0.0 | 0.54 Comm | 0.012028 | 0.012106 | 0.012183 | 0.1 | 1.48 Output | 0.00018858 | 0.00019606 | 0.00020354 | 0.0 | 0.02 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004508 | | | 0.55 Nlocal: 144 ave 145 max 143 min Histogram: 1 0 0 0 0 0 0 0 0 1 Nghost: 2551 ave 2553 max 2549 min Histogram: 1 0 0 0 0 0 0 0 0 1 Neighs: 29878.5 ave 30155 max 29602 min Histogram: 1 0 0 0 0 0 0 0 0 1 Total # of neighbors = 59757 Ave neighs/atom = 207.48958 Ave special neighs/atom = 2.3333333 Neighbor list builds = 4 Dangerous builds = 0 undump sci Total wall time: 0:00:00