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 = 0.011 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) change_box all triclinic Changing box ... triclinic box = (0 0 0) to (9.975 7.186 23.982633) with tilt (0 -3.704136 0) kspace_style pppm 0.00001 fix 2_2_1 all box/relax x 0.987 y 0.987 z 0.987 yz 0.000 xz 0.000 xy 0.000 couple none vmax 0.01 dilate all 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 WARNING: Energy due to 6 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 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 -2.6112446e-13 1.7763568e-13 -3.19373e-13 4 9206958.5 15455834 89423259 1762.3041 1.7221307 -2424478.2 -75406692 -1.9043861e+08 -1.1989892e+08 -21648889 -13626504 758045.08 9.8937086 7.0827175 25.578295 1.5707963 1.7542532 1.5707963 -4.1819703e-10 6.981935e-09 4.6903921e-09 WARNING: Bond/angle/dihedral extent > half of periodic box length (../domain.cpp:935) Loop time of 0.135916 on 2 procs for 4 steps with 192 atoms 97.9% CPU use with 2 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero Energy initial, next-to-last, final = -5870.53076385731 -6001.05331451141 758045.084484991 Force two-norm initial, final = 2222.0471 16297431 Force max component initial, final = 1670.4662 9206958.5 Final line search alpha, max atom move = 1.4087487e-54 1.2970291e-47 Iterations, force evaluations = 4 56 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.050335 | 0.050381 | 0.050427 | 0.0 | 37.07 Bond | 0.00039446 | 0.00039782 | 0.00040119 | 0.0 | 0.29 Kspace | 0.037601 | 0.037657 | 0.037712 | 0.0 | 27.71 Neigh | 0.0052094 | 0.0052119 | 0.0052144 | 0.0 | 3.83 Comm | 0.0052031 | 0.0052261 | 0.0052491 | 0.0 | 3.85 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03704 | | | 27.25 Nlocal: 96 ave 96 max 96 min Histogram: 2 0 0 0 0 0 0 0 0 0 Nghost: 3887 ave 3887 max 3887 min Histogram: 2 0 0 0 0 0 0 0 0 0 Neighs: 33765 ave 33766 max 33764 min Histogram: 1 0 0 0 0 0 0 0 0 1 Total # of neighbors = 67530 Ave neighs/atom = 351.71875 Ave special neighs/atom = 2.3333333 Neighbor list builds = 4 Dangerous builds = 3 undump sci unfix 2_2_1 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 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) = 0.34863872 grid = 15 10 30 stencil order = 5 estimated absolute RMS force accuracy = 0.0011945758 estimated relative force accuracy = 3.5974297e-06 using double precision KISS FFT 3d grid and FFT values/proc = 8976 2250 generated 0 of 10 mixed pair_coeff terms from sixthpower mixing rule Setting up cg style minimization ... Unit style : real Current step : 0 WARNING: Bond/angle/dihedral extent > half of periodic box length (../domain.cpp:935) Per MPI rank memory allocation (min/avg/max) = 12.71 | 12.71 | 12.71 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 9206958.5 15455834 89423260 1762.3041 1.7221307 -2424478.8 -75406695 -1.9043861e+08 -1.1989892e+08 -21648890 -13626504 758045.09 9.8937086 7.0827175 25.578295 1.5707963 1.7542532 1.5707963 -1.1146994e-10 1.185208e-08 1.9909209e-08 100 1.7998805 7.3222384 -26749.77 1762.3041 1.7221307 21673.023 37766.385 20809.901 -331.54597 -2574.2163 857.78513 -6478.0389 9.8937086 7.0827175 25.578295 1.5707963 1.7542532 1.5707963 -7.0166095e-14 5.4378724e-13 4.4941828e-13 200 1.7074839 6.8652206 -26220.893 1762.3041 1.7221307 23147.872 37156.284 18358.523 -4311.916 -2448.5955 1785.9819 -6490.9135 9.8937086 7.0827175 25.578295 1.5707963 1.7542532 1.5707963 7.2386541e-14 4.5297099e-13 -1.2256862e-13 248 0.24202438 0.93920209 -26603.335 1762.3041 1.7221307 23545.988 37601.751 18662.266 -4268.8106 -2420.3508 1678.3473 -6491.4433 9.8937086 7.0827175 25.578295 1.5707963 1.7542532 1.5707963 2.8499772e-13 -2.1049829e-13 4.2355008e-14 Loop time of 0.733245 on 2 procs for 248 steps with 192 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 = 758045.088618318 -6491.44405473089 -6491.44333740204 Force two-norm initial, final = 15455834 0.93920209 Force max component initial, final = 9206958.5 0.24202438 Final line search alpha, max atom move = 0.0013544325 0.0003278057 Iterations, force evaluations = 248 488 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.37922 | 0.38553 | 0.39185 | 1.0 | 52.58 Bond | 0.0026654 | 0.0027145 | 0.0027636 | 0.1 | 0.37 Kspace | 0.29397 | 0.30041 | 0.30686 | 1.2 | 40.97 Neigh | 0.0073076 | 0.0073101 | 0.0073126 | 0.0 | 1.00 Comm | 0.031509 | 0.031682 | 0.031855 | 0.1 | 4.32 Output | 0.00017822 | 0.0001844 | 0.00019058 | 0.0 | 0.03 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005409 | | | 0.74 Nlocal: 96 ave 97 max 95 min Histogram: 1 0 0 0 0 0 0 0 0 1 Nghost: 3813 ave 3819 max 3807 min Histogram: 1 0 0 0 0 0 0 0 0 1 Neighs: 33105 ave 33157 max 33053 min Histogram: 1 0 0 0 0 0 0 0 0 1 Total # of neighbors = 66210 Ave neighs/atom = 344.84375 Ave special neighs/atom = 2.3333333 Neighbor list builds = 6 Dangerous builds = 0 undump sci Total wall time: 0:00:01