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 = 4.0446508 4.0446508 4.0446508 Created orthogonal box = (0.0000000 -43.566267 0.0000000) to (21.781111 43.566267 4.0446508) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.2575096 5.2575096 4.0446508 Created 233 atoms using lattice units in orthogonal box = (0.0000000 -43.566267 0.0000000) to (21.781111 43.566267 4.0446508) create_atoms CPU = 0.002 seconds 233 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.2575096 5.2575096 4.0446508 Created 233 atoms using lattice units in orthogonal box = (0.0000000 -43.566267 0.0000000) to (21.781111 43.566267 4.0446508) create_atoms CPU = 0.001 seconds 233 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 = 6.7 ghost atom cutoff = 6.7 binsize = 3.35, bins = 7 27 2 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 6.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 10 atoms, new total = 456 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_127847080751_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 = 6.7 ghost atom cutoff = 6.7 binsize = 3.35, bins = 7 27 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.7 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) = 4.457 | 4.457 | 4.457 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1518.8323 0 -1518.8323 -516.75409 49 0 -1525.3597 0 -1525.3597 -7720.0299 Loop time of 3.34037 on 1 procs for 49 steps with 456 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 = -1518.83231490901 -1525.35828538743 -1525.35966074075 Force two-norm initial, final = 9.7874327 0.091489235 Force max component initial, final = 2.8500790 0.017761055 Final line search alpha, max atom move = 1.0000000 0.017761055 Iterations, force evaluations = 49 86 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.3211 | 3.3211 | 3.3211 | 0.0 | 99.42 Neigh | 0.0055523 | 0.0055523 | 0.0055523 | 0.0 | 0.17 Comm | 0.0070525 | 0.0070525 | 0.0070525 | 0.0 | 0.21 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006644 | | | 0.20 Nlocal: 456.000 ave 456 max 456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3290.00 ave 3290 max 3290 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: 35052.0 ave 35052 max 35052 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 35052 Ave neighs/atom = 76.868421 Neighbor list builds = 1 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 = 6.7 ghost atom cutoff = 6.7 binsize = 3.35, bins = 7 27 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 49 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.454 | 4.454 | 4.454 Mbytes Step Temp E_pair E_mol TotEng Press Volume 49 0 -1525.3597 0 -1525.3597 -7720.0299 7676.1139 55 0 -1525.523 0 -1525.523 -1014.7184 7608.8346 Loop time of 0.306353 on 1 procs for 6 steps with 456 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1525.35966074075 -1525.52241808417 -1525.52304177161 Force two-norm initial, final = 51.244233 0.36659959 Force max component initial, final = 38.515730 0.24792242 Final line search alpha, max atom move = 0.00073179787 0.00018142910 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.30386 | 0.30386 | 0.30386 | 0.0 | 99.19 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00052042 | 0.00052042 | 0.00052042 | 0.0 | 0.17 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001969 | | | 0.64 Nlocal: 456.000 ave 456 max 456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2960.00 ave 2960 max 2960 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: 35142.0 ave 35142 max 35142 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 35142 Ave neighs/atom = 77.065789 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 = 6.7 ghost atom cutoff = 6.7 binsize = 3.35, bins = 7 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.7 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) = 4.592 | 4.592 | 4.592 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1525.523 0 -1525.523 -1014.7184 Loop time of 7.046e-06 on 1 procs for 0 steps with 456 atoms 170.3% 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 | | 7.046e-06 | | |100.00 Nlocal: 456.000 ave 456 max 456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2960.00 ave 2960 max 2960 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: 35150.0 ave 35150 max 35150 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 35150 Ave neighs/atom = 77.083333 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 = 6.7 ghost atom cutoff = 6.7 binsize = 3.35, bins = 7 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.7 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) = 4.592 | 4.592 | 4.592 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 -1525.523 -1525.523 21.708509 87.132534 4.0226088 -1014.7184 -1014.7184 -48.525229 -2943.7101 -51.920011 2.5536878 346.74448 Loop time of 6.625e-06 on 1 procs for 0 steps with 456 atoms 241.5% 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 | | 6.625e-06 | | |100.00 Nlocal: 456.000 ave 456 max 456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2960.00 ave 2960 max 2960 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 17575.0 ave 17575 max 17575 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 35150.0 ave 35150 max 35150 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 35150 Ave neighs/atom = 77.083333 Neighbor list builds = 0 Dangerous builds = 0 456 -1525.52304177161 eV 2.55368781785205 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04