LAMMPS (30 Jul 2021) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 3.6110985 3.6110985 3.6110985 Created orthogonal box = (0.0000000 -43.633070 0.0000000) to (53.439378 43.633070 8.8453488) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1243239 5.3794195 5.8968992 Created 1751 atoms using lattice units in orthogonal box = (0.0000000 -43.633070 0.0000000) to (53.439378 43.633070 8.8453488) create_atoms CPU = 0.002 seconds 1751 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1243239 5.3794195 5.8968992 Created 1757 atoms using lattice units in orthogonal box = (0.0000000 -43.633070 0.0000000) to (53.439378 43.633070 8.8453488) create_atoms CPU = 0.002 seconds 1757 atoms in group lower Displacing atoms ... System init for delete_atoms ... Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 16 26 3 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) command delete_atoms, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) pair kim, perpetual attributes: full, newton off, cut 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 11 atoms, new total = 3497 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Your simulation uses code contributions which should be cited: - OpenKIM: https://doi.org/10.1007/s11837-011-0102-6 - OpenKIM potential: https://openkim.org/cite/MO_260546967793_001#item-citation The log file lists these citations in BibTeX format. CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 16 26 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 6.522 | 6.522 | 6.522 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13703.765 0 -13703.765 56258.178 252 0 -14802.343 0 -14802.343 2692.0898 Loop time of 103.825 on 1 procs for 252 steps with 3497 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -13703.7647163537 -14802.3291382287 -14802.3431636035 Force two-norm initial, final = 1021.7059 0.40472411 Force max component initial, final = 176.49499 0.11479225 Final line search alpha, max atom move = 0.81262004 0.093282485 Iterations, force evaluations = 252 468 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 103.48 | 103.48 | 103.48 | 0.0 | 99.67 Neigh | 0.21158 | 0.21158 | 0.21158 | 0.0 | 0.20 Comm | 0.055783 | 0.055783 | 0.055783 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.08001 | | | 0.08 Nlocal: 3497.00 ave 3497 max 3497 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9404.00 ave 9404 max 9404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 417066.0 ave 417066 max 417066 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 417066 Ave neighs/atom = 119.26394 Neighbor list builds = 7 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 16 26 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 252 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.520 | 6.520 | 6.520 Mbytes Step Temp E_pair E_mol TotEng Press Volume 252 0 -14802.343 0 -14802.343 2692.0898 41249.826 264 0 -14805.039 0 -14805.039 -1.8045749 41308.02 Loop time of 3.10902 on 1 procs for 12 steps with 3497 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -14802.3431636036 -14805.0359880365 -14805.0393417182 Force two-norm initial, final = 397.72065 1.3998317 Force max component initial, final = 287.77821 0.30773717 Final line search alpha, max atom move = 0.00010709432 3.2956904e-05 Iterations, force evaluations = 12 13 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.0999 | 3.0999 | 3.0999 | 0.0 | 99.71 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0010981 | 0.0010981 | 0.0010981 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008073 | | | 0.26 Nlocal: 3497.00 ave 3497 max 3497 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9392.00 ave 9392 max 9392 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 417342.0 ave 417342 max 417342 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 417342 Ave neighs/atom = 119.34287 Neighbor list builds = 0 Dangerous builds = 0 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 16 26 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) compute centro/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) compute pair/local, occasional attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 6.658 | 6.658 | 6.658 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14805.039 0 -14805.039 -1.8045749 Loop time of 2.35e-06 on 1 procs for 0 steps with 3497 atoms 170.2% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 2.35e-06 | | |100.00 Nlocal: 3497.00 ave 3497 max 3497 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9378.00 ave 9378 max 9378 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 411176.0 ave 411176 max 411176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 411176 Ave neighs/atom = 117.57964 Neighbor list builds = 0 Dangerous builds = 0 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 16 26 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) compute centro/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) compute pair/local, occasional attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 6.658 | 6.658 | 6.658 Mbytes Step v_pe_metal c_particle_engsum v_lx_metal v_ly_metal v_lz_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_mindist_metal v_csymsum_metal 0 -14805.039 -14805.039 52.844449 87.797524 8.9033355 -1.8045749 -1.8045749 -7.550523 -9.87737 12.014168 2.2946202 5516.1293 Loop time of 2.672e-06 on 1 procs for 0 steps with 3497 atoms 262.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 2.672e-06 | | |100.00 Nlocal: 3497.00 ave 3497 max 3497 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9378.00 ave 9378 max 9378 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 205588.0 ave 205588 max 205588 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 411176.0 ave 411176 max 411176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 411176 Ave neighs/atom = 117.57964 Neighbor list builds = 0 Dangerous builds = 0 3497 -14805.0393417182 eV 2.29462022417875 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:01:48