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 = 2.8552797 2.8552797 2.8552797 Created orthogonal box = (0.0000000 -29.946426 0.0000000) to (36.676732 29.946426 6.9939784) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.6679477 4.3558438 4.6626523 Created 657 atoms using lattice units in orthogonal box = (0.0000000 -29.946426 0.0000000) to (36.676732 29.946426 6.9939784) create_atoms CPU = 0.001 seconds 657 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.6679477 4.3558438 4.6626523 Created 663 atoms using lattice units in orthogonal box = (0.0000000 -29.946426 0.0000000) to (36.676732 29.946426 6.9939784) create_atoms CPU = 0.001 seconds 663 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 = 7.8 ghost atom cutoff = 7.8 binsize = 3.9, bins = 10 16 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 7.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 9 atoms, new total = 1311 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_466808877130_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 = 7.8 ghost atom cutoff = 7.8 binsize = 3.9, bins = 10 16 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.8 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) = 5.474 | 5.474 | 5.474 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3885.7254 0 -3885.7254 219685.82 102 0 -5361.2914 0 -5361.2914 -8483.294 Loop time of 2.35321 on 1 procs for 102 steps with 1311 atoms 98.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3885.72543720744 -5361.28609016162 -5361.29136500307 Force two-norm initial, final = 1915.8868 0.47230083 Force max component initial, final = 300.58430 0.14594087 Final line search alpha, max atom move = 0.56747699 0.082818083 Iterations, force evaluations = 102 182 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.2933 | 2.2933 | 2.2933 | 0.0 | 97.46 Neigh | 0.026837 | 0.026837 | 0.026837 | 0.0 | 1.14 Comm | 0.017601 | 0.017601 | 0.017601 | 0.0 | 0.75 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01544 | | | 0.66 Nlocal: 1311.00 ave 1311 max 1311 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6502.00 ave 6502 max 6502 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: 219178.0 ave 219178 max 219178 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 219178 Ave neighs/atom = 167.18383 Neighbor list builds = 2 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 = 7.8 ghost atom cutoff = 7.8 binsize = 3.9, bins = 10 16 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 102 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.474 | 5.474 | 5.474 Mbytes Step Temp E_pair E_mol TotEng Press Volume 102 0 -5361.2914 0 -5361.2914 -8483.294 15363.491 107 0 -5361.577 0 -5361.577 0.81374801 15289.369 Loop time of 0.105498 on 1 procs for 5 steps with 1311 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 = -5361.29136500308 -5361.57661494971 -5361.57704805132 Force two-norm initial, final = 152.41443 0.85814123 Force max component initial, final = 112.15002 0.50841608 Final line search alpha, max atom move = 0.00019558786 9.9440012e-05 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.10262 | 0.10262 | 0.10262 | 0.0 | 97.27 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00044186 | 0.00044186 | 0.00044186 | 0.0 | 0.42 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002435 | | | 2.31 Nlocal: 1311.00 ave 1311 max 1311 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6509.00 ave 6509 max 6509 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: 219658.0 ave 219658 max 219658 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 219658 Ave neighs/atom = 167.54996 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 = 7.8 ghost atom cutoff = 7.8 binsize = 3.9, bins = 10 16 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.8 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) = 5.612 | 5.612 | 5.612 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5361.577 0 -5361.577 0.81374801 Loop time of 2.199e-06 on 1 procs for 0 steps with 1311 atoms 181.9% 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 | | 2.199e-06 | | |100.00 Nlocal: 1311.00 ave 1311 max 1311 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6506.00 ave 6506 max 6506 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: 219826.0 ave 219826 max 219826 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 219826 Ave neighs/atom = 167.67811 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 = 7.8 ghost atom cutoff = 7.8 binsize = 3.9, bins = 10 16 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.8 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) = 5.612 | 5.612 | 5.612 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 -5361.577 -5361.577 36.708201 59.697828 6.9769874 0.81374801 0.81374801 -24.946003 -25.76036 53.147607 2.2167073 1538.9045 Loop time of 2.613e-06 on 1 procs for 0 steps with 1311 atoms 229.6% 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 | | 2.613e-06 | | |100.00 Nlocal: 1311.00 ave 1311 max 1311 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6506.00 ave 6506 max 6506 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 109913.0 ave 109913 max 109913 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 219826.0 ave 219826 max 219826 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 219826 Ave neighs/atom = 167.67811 Neighbor list builds = 0 Dangerous builds = 0 1311 -5361.57704805132 eV 2.21670726700387 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03