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 ... orthogonal box = (0 0 0) to (5.64056 5.64056 5.64056) 1 by 2 by 2 MPI processor grid reading atoms ... 8 atoms Finding 1-2 1-3 1-4 neighbors ... special bond factors lj: 0 0 1 special bond factors coul: 0 0 1 0 = max # of 1-2 neighbors 0 = max # of 1-3 neighbors 1 = max # of special neighbors special bonds CPU = 0.000 seconds read_data CPU = 0.004 seconds include parameters.dat bond_coeff 1 0.0000 0.0000 0.0000 0.0000 # xxx xxx angle_coeff 1 0.0000 0.0000 0.0000 0.0000 # xxx xxx xxx dihedral_coeff 1 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 # xxx xxx xxx xxx improper_coeff 1 0.0 0.0 # xxx xxx xxx xxx angle_coeff 1 bb 0.0 0.0 0.0 # xxx xxx xxx angle_coeff 1 ba 0.0 0.0 0.0 0.0 # xxx xxx xxx 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 # xxx xxx xxx xxx pair_coeff 1 1 0.05899 5.1728 # Cl - pair_coeff 2 2 0.3828 2.494 # Na+ - 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 8 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 ... using 12-bit tables for long-range coulomb (../kspace.cpp:340) G vector (1/distance) = 0.2765886 grid = 6 6 6 stencil order = 5 estimated absolute RMS force accuracy = 0.00094138881 estimated relative force accuracy = 2.8349644e-06 using double precision KISS FFT 3d grid and FFT values/proc = 1300 72 generated 0 of 1 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 = 1 1 1 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 stencil: half/bin/3d bin: standard Setting up cg style minimization ... Unit style : real Current step : 0 Per MPI rank memory allocation (min/avg/max) = 8.783 | 8.784 | 8.785 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 1.1657342e-14 1.6039829e-14 28524.392 179.45959 2.1630931 -28524.392 -28524.392 -28524.392 -4.0722919e-12 -1.0859445e-11 -2.7148613e-12 -732.41929 5.64056 5.64056 5.64056 1.5707963 1.5707963 1.5707963 3.1086245e-15 -1.625089e-14 7.6501305e-16 Exceeded microiterations, alpha = 0.020000000, slope is 0.000000000, started at -0.000000000 Exceeded microiterations, alpha = 0.020000000, slope is 0.000000000, started at -0.000000000 Exceeded microiterations, alpha = 0.020000000, slope is 0.000000000, started at -0.000000000 Exceeded microiterations, alpha = 0.020000000, slope is 0.000000000, started at -0.000000000 1 2.5757174e-14 3.8088938e-14 28524.392 179.45959 2.1630931 -28524.392 -28524.392 -28524.392 -5.4297226e-12 -1.0859445e-11 -1.3574306e-12 -732.41929 5.64056 5.64056 5.64056 1.5707963 1.5707963 1.5707963 1.831868e-15 -1.4085955e-14 2.4303476e-15 Loop time of 0.00807538 on 4 procs for 1 steps with 8 atoms 99.3% CPU use with 4 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = force tolerance Energy initial, next-to-last, final = -732.419293351377 -732.419293351377 -732.419293351377 Force two-norm initial, final = 1.6039829e-14 3.8088938e-14 Force max component initial, final = 1.1657342e-14 2.5757174e-14 Final line search alpha, max atom move = 0.02 5.1514348e-16 Iterations, force evaluations = 1 51 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.00063443 | 0.00078129 | 0.00094721 | 0.0 | 9.68 Bond | 2.5011e-05 | 2.6642e-05 | 2.7655e-05 | 0.0 | 0.33 Kspace | 0.0034834 | 0.0036208 | 0.0037438 | 0.2 | 44.84 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0030371 | 0.0030756 | 0.0031075 | 0.0 | 38.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0005711 | | | 7.07 Nlocal: 2 ave 2 max 2 min Histogram: 4 0 0 0 0 0 0 0 0 0 Nghost: 1098 ave 1098 max 1098 min Histogram: 4 0 0 0 0 0 0 0 0 0 Neighs: 484 ave 565 max 403 min Histogram: 1 1 0 0 0 0 0 0 1 1 Total # of neighbors = 1936 Ave neighs/atom = 242 Ave special neighs/atom = 0 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 change_box all triclinic Changing box ... triclinic box = (0 0 0) to (5.64056 5.64056 5.64056) with tilt (0 0 0) kspace_style pppm 0.00001 fix 2_3_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 2.3.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) = 0.29166098 grid = 8 8 8 stencil order = 5 estimated absolute RMS force accuracy = 0.00027054584 estimated relative force accuracy = 8.1474075e-07 using double precision KISS FFT 3d grid and FFT values/proc = 1815 128 generated 0 of 1 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 = 1 1 1 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) = 8.821 | 8.821 | 8.821 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 8.437695e-15 1.5064248e-14 28516.873 179.45959 2.1630931 -28516.873 -28516.873 -28516.873 -1.478113e-11 -1.8590566e-11 2.8110419e-13 -732.42171 5.64056 5.64056 5.64056 1.5707963 1.5707963 1.5707963 -1.3378187e-14 -1.6653345e-15 2.1316282e-14 2 1.5987212e-14 2.6471748e-14 8.8628073 193.78536 2.0031844 -8.8628073 -8.8628073 -8.8628073 2.1254894e-12 -2.852025e-13 -1.5730079e-12 -735.12413 5.7868246 5.7868246 5.7868246 1.5707963 1.5707963 1.5707963 3.7206349e-14 -2.7200464e-15 1.3183898e-15 Loop time of 0.00117762 on 4 procs for 2 steps with 8 atoms 99.8% CPU use with 4 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = force tolerance Energy initial, next-to-last, final = -732.421708277846 -735.098180393796 -735.123928229352 Force two-norm initial, final = 129.26771 0.037578069 Force max component initial, final = 74.632748 0.021695708 Final line search alpha, max atom move = 0.00040629915 8.8149479e-06 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8.2069e-05 | 8.6595e-05 | 9.088e-05 | 0.0 | 7.35 Bond | 2.915e-06 | 3.1332e-06 | 3.349e-06 | 0.0 | 0.27 Kspace | 0.00041066 | 0.00041917 | 0.00042836 | 0.0 | 35.59 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00025758 | 0.00026233 | 0.00026666 | 0.0 | 22.28 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0004064 | | | 34.51 Nlocal: 2 ave 2 max 2 min Histogram: 4 0 0 0 0 0 0 0 0 0 Nghost: 1098 ave 1098 max 1098 min Histogram: 4 0 0 0 0 0 0 0 0 0 Neighs: 484 ave 516 max 452 min Histogram: 1 0 0 0 0 2 0 0 0 1 Total # of neighbors = 1936 Ave neighs/atom = 242 Ave special neighs/atom = 0 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 2_3_1 Total wall time: 0:00:00