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 = 3.5200008 3.5200008 3.5200008 Created orthogonal box = (0.0000000 -41.649211 0.0000000) to (51.009657 41.649211 8.6222058) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8296751 5.3548985 5.7481372 Created 1662 atoms using lattice units in orthogonal box = (0.0000000 -41.649211 0.0000000) to (51.009657 41.649211 8.6222058) create_atoms CPU = 0.003 seconds 1662 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8296751 5.3548985 5.7481372 Created 1686 atoms using lattice units in orthogonal box = (0.0000000 -41.649211 0.0000000) to (51.009657 41.649211 8.6222058) create_atoms CPU = 0.003 seconds 1686 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 14 22 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 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 30 atoms, new total = 3318 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_803527979660_000#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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 14 22 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 6.981 | 6.981 | 6.981 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14576.594 0 -14576.594 -5478.2439 215 0 -14687.446 0 -14687.446 -12484.238 Loop time of 11.1475 on 1 procs for 215 steps with 3318 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 = -14576.5942515152 -14687.4339177391 -14687.4459848917 Force two-norm initial, final = 33.722849 0.49519188 Force max component initial, final = 3.9603192 0.097199810 Final line search alpha, max atom move = 0.87374691 0.084928035 Iterations, force evaluations = 215 404 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 10.794 | 10.794 | 10.794 | 0.0 | 96.83 Neigh | 0.2438 | 0.2438 | 0.2438 | 0.0 | 2.19 Comm | 0.045768 | 0.045768 | 0.045768 | 0.0 | 0.41 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.06436 | | | 0.58 Nlocal: 3318.00 ave 3318 max 3318 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10903.0 ave 10903 max 10903 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: 583080.0 ave 583080 max 583080 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 583080 Ave neighs/atom = 175.73237 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 14 22 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 215 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.982 | 6.982 | 6.982 Mbytes Step Temp E_pair E_mol TotEng Press Volume 215 0 -14687.446 0 -14687.446 -12484.238 36635.959 220 0 -14688.589 0 -14688.589 -376.85419 36400.755 Loop time of 0.189929 on 1 procs for 5 steps with 3318 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -14687.4459848917 -14688.5748904564 -14688.5891172449 Force two-norm initial, final = 513.83793 16.642033 Force max component initial, final = 398.52696 14.517246 Final line search alpha, max atom move = 3.4353191e-05 0.00049871372 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.18548 | 0.18548 | 0.18548 | 0.0 | 97.66 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00062577 | 0.00062577 | 0.00062577 | 0.0 | 0.33 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003821 | | | 2.01 Nlocal: 3318.00 ave 3318 max 3318 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10873.0 ave 10873 max 10873 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: 582906.0 ave 582906 max 582906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 582906 Ave neighs/atom = 175.67993 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 14 22 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 7.120 | 7.120 | 7.120 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14688.589 0 -14688.589 -376.85419 Loop time of 2.307e-06 on 1 procs for 0 steps with 3318 atoms 173.4% 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 | | 2.307e-06 | | |100.00 Nlocal: 3318.00 ave 3318 max 3318 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10906.0 ave 10906 max 10906 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: 584290.0 ave 584290 max 584290 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 584290 Ave neighs/atom = 176.09705 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 14 22 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 7.120 | 7.120 | 7.120 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 -14688.589 -14688.589 50.967038 82.93808 8.6112662 -376.85419 -376.85419 -296.19765 -636.21135 -198.15358 2.2385116 1616.8532 Loop time of 2.481e-06 on 1 procs for 0 steps with 3318 atoms 282.1% 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 | | 2.481e-06 | | |100.00 Nlocal: 3318.00 ave 3318 max 3318 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10906.0 ave 10906 max 10906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 292145.0 ave 292145 max 292145 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 584290.0 ave 584290 max 584290 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 584290 Ave neighs/atom = 176.09705 Neighbor list builds = 0 Dangerous builds = 0 3318 -14688.5891172449 eV 2.2385116280443 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:12