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 22.8) with tilt (-4.666103 0 0) 1 by 2 by 1 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 = 0.009 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 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) = 0.33551858 grid = 12 27 24 stencil order = 5 estimated absolute RMS force accuracy = 0.0014989736 estimated relative force accuracy = 4.5141144e-06 using double precision KISS FFT 3d grid and FFT values/proc = 12369 4032 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 4 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) = 12.84 | 12.85 | 12.86 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 0 244.31484 1652.7295 -81053.369 5673.0468 0.53497144 87585.044 70424.064 85151 -2296.4228 265.29654 1000.6639 -4784.5539 9.89371 25.5783 22.8 1.5707963 1.5707963 1.7542479 -1.4210855e-14 -2.8421709e-14 2.4868996e-13 100 3.0528323 15.977743 -2734.1701 5673.0468 0.53497144 6594.7041 1653.3602 -45.554034 81.830037 -36.361564 -926.46655 -6270.5288 9.89371 25.5783 22.8 1.5707963 1.5707963 1.7542479 1.7230661e-13 -5.2802207e-13 4.8849813e-14 200 0.21301429 1.5298824 -2576.1629 5673.0468 0.53497144 6443.8095 1199.6685 85.010534 9.2112079 -3.4091351 -661.54039 -6274.0536 9.89371 25.5783 22.8 1.5707963 1.5707963 1.7542479 1.7263968e-14 2.6090241e-14 1.7297275e-13 225 0.14179393 0.97674097 -2566.8748 5673.0468 0.53497144 6423.5554 1169.8462 107.22272 -10.88212 -0.76541569 -673.34483 -6274.0859 9.89371 25.5783 22.8 1.5707963 1.5707963 1.7542479 -1.3984647e-13 1.1250723e-13 2.0422553e-13 Loop time of 0.578152 on 2 procs for 225 steps with 192 atoms 99.3% CPU use with 2 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = force tolerance Energy initial, next-to-last, final = -4784.55394511616 -6274.08511261572 -6274.08591110258 Force two-norm initial, final = 1652.7295 0.97674097 Force max component initial, final = 244.31484 0.14179393 Final line search alpha, max atom move = 0.0013893555 0.00019700218 Iterations, force evaluations = 225 410 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.16151 | 0.16655 | 0.1716 | 1.2 | 28.81 Bond | 0.003054 | 0.0030576 | 0.0030612 | 0.0 | 0.53 Kspace | 0.38744 | 0.39244 | 0.39744 | 0.8 | 67.88 Neigh | 0.0021326 | 0.0021381 | 0.0021436 | 0.0 | 0.37 Comm | 0.0093981 | 0.0094957 | 0.0095933 | 0.1 | 1.64 Output | 0.00017243 | 0.00017775 | 0.00018308 | 0.0 | 0.03 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004287 | | | 0.74 Nlocal: 96 ave 96 max 96 min Histogram: 2 0 0 0 0 0 0 0 0 0 Nghost: 1751.5 ave 1758 max 1745 min Histogram: 1 0 0 0 0 0 0 0 0 1 Neighs: 14341 ave 14756 max 13926 min Histogram: 1 0 0 0 0 0 0 0 0 1 Total # of neighbors = 28682 Ave neighs/atom = 149.38542 Ave special neighs/atom = 2.3333333 Neighbor list builds = 3 Dangerous builds = 0 undump sci Total wall time: 0:00:00