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 12 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 (9.75106 24.069413 33.27397) with tilt (-4.342482 0 0) 1 by 1 by 2 MPI processor grid reading atoms ... 480 atoms scanning bonds ... 1 = max bonds/atom scanning angles ... 6 = max angles/atom scanning impropers ... 4 = max impropers/atom reading bonds ... 320 bonds reading angles ... 240 angles reading impropers ... 80 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 = 0.011 seconds include parameters.dat bond_coeff 1 1.5325 277.56 -433.25 2922.8 # o1S- s4o- bond_coeff 2 0.97 563.28 -1428.2 1902.1 # h* o* 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 480 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 = 0.002 (../kspace.cpp:325) using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.26666025 grid = 12 24 24 stencil order = 5 estimated absolute RMS force accuracy = 0.0016600455 estimated relative force accuracy = 4.9991778e-06 using double precision KISS FFT 3d grid and FFT values/proc = 11191 3456 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 = 14 ghost atom cutoff = 14 binsize = 7, bins = 3 4 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) = 13.05 | 13.25 | 13.44 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 55.510554 418.14043 -2604.9821 7809.477 0.97154971 2659.9963 -2232.5624 7387.5123 226.38613 892.67549 720.64899 -15763.655 9.75106 24.458001 33.27397 1.5707963 1.5707963 1.7492912 -4.7606363e-13 3.723688e-13 -4.8672177e-13 100 1.559394 9.1331591 305.84481 7809.477 0.97154971 3157.9737 -3508.3484 -567.15977 -24.584949 2.1600211 -902.7075 -16057.447 9.75106 24.458001 33.27397 1.5707963 1.5707963 1.7492912 3.9571124e-13 1.2012613e-12 3.1086245e-13 200 0.30308689 1.6511989 -406.93426 7809.477 0.97154971 4674.7655 -3614.8661 160.90339 1.0123938 0.37254135 -679.62445 -16067.913 9.75106 24.458001 33.27397 1.5707963 1.5707963 1.7492912 7.5298101e-13 9.1118779e-13 -1.174616e-13 209 0.10796737 0.93316318 -394.4222 7809.477 0.97154971 4670.1963 -3636.0261 149.09632 -1.9261951 -9.1105414 -690.68255 -16067.927 9.75106 24.458001 33.27397 1.5707963 1.5707963 1.7492912 3.01148e-13 6.594586e-13 6.2660988e-13 Loop time of 1.83003 on 2 procs for 209 steps with 480 atoms 99.2% CPU use with 2 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = force tolerance Energy initial, next-to-last, final = -15763.6550527412 -16067.9263122959 -16067.9267126869 Force two-norm initial, final = 418.14043 0.93316318 Force max component initial, final = 55.510554 0.10796737 Final line search alpha, max atom move = 0.001574125 0.00016995413 Iterations, force evaluations = 209 392 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.67448 | 1.0333 | 1.3921 | 35.3 | 56.46 Bond | 0.0048455 | 0.004868 | 0.0048904 | 0.0 | 0.27 Kspace | 0.37734 | 0.7358 | 1.0943 | 41.8 | 40.21 Neigh | 0.011994 | 0.011998 | 0.012001 | 0.0 | 0.66 Comm | 0.036597 | 0.037515 | 0.038433 | 0.5 | 2.05 Output | 0.00019148 | 0.00019732 | 0.00020315 | 0.0 | 0.01 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006386 | | | 0.35 Nlocal: 240 ave 241 max 239 min Histogram: 1 0 0 0 0 0 0 0 0 1 Nghost: 5228 ave 5229 max 5227 min Histogram: 1 0 0 0 0 0 0 0 0 1 Neighs: 113722 ave 157728 max 69717 min Histogram: 1 0 0 0 0 0 0 0 0 1 Total # of neighbors = 227445 Ave neighs/atom = 473.84375 Ave special neighs/atom = 2.3333333 Neighbor list builds = 3 Dangerous builds = 0 undump sci Total wall time: 0:00:01