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 = 3.0829274 3.0829274 3.0829274 Created orthogonal box = (0.0000000 -40.435296 0.0000000) to (28.589892 40.435296 4.3599177) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3190497 5.1715622 4.3599177 Created 345 atoms using lattice units in orthogonal box = (0.0000000 -40.435296 0.0000000) to (28.589892 40.435296 4.3599177) create_atoms CPU = 0.001 seconds 345 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.3190497 5.1715622 4.3599177 Created 345 atoms using lattice units in orthogonal box = (0.0000000 -40.435296 0.0000000) to (28.589892 40.435296 4.3599177) create_atoms CPU = 0.001 seconds 345 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 9 25 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, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 0 atoms, new total = 690 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_152208847456_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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 9 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 5.276 | 5.276 | 5.276 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4137.609 0 -4137.609 139881.42 122 0 -4478.8322 0 -4478.8322 8862.594 Loop time of 40.9545 on 1 procs for 122 steps with 690 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 = -4137.60903682117 -4478.82851455889 -4478.83218348624 Force two-norm initial, final = 369.90569 0.29229452 Force max component initial, final = 75.509223 0.094277231 Final line search alpha, max atom move = 1.0000000 0.094277231 Iterations, force evaluations = 122 232 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 40.876 | 40.876 | 40.876 | 0.0 | 99.81 Neigh | 0.063537 | 0.063537 | 0.063537 | 0.0 | 0.16 Comm | 0.0079412 | 0.0079412 | 0.0079412 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007009 | | | 0.02 Nlocal: 690.000 ave 690 max 690 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4010.00 ave 4010 max 4010 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: 51356.0 ave 51356 max 51356 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 51356 Ave neighs/atom = 74.428986 Neighbor list builds = 3 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 9 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 122 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.276 | 5.276 | 5.276 Mbytes Step Temp E_pair E_mol TotEng Press Volume 122 0 -4478.8322 0 -4478.8322 8862.594 10080.485 129 0 -4479.2762 0 -4479.2762 1279.8628 10114.878 Loop time of 1.74971 on 1 procs for 7 steps with 690 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4478.83218348625 -4479.27611441892 -4479.2762025058 Force two-norm initial, final = 146.70852 1.1742087 Force max component initial, final = 145.91464 0.43796495 Final line search alpha, max atom move = 0.00069401848 0.00030395577 Iterations, force evaluations = 7 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.748 | 1.748 | 1.748 | 0.0 | 99.90 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0003017 | 0.0003017 | 0.0003017 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00141 | | | 0.08 Nlocal: 690.000 ave 690 max 690 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4022.00 ave 4022 max 4022 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: 52300.0 ave 52300 max 52300 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 52300 Ave neighs/atom = 75.797101 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 9 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/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) = 5.414 | 5.414 | 5.414 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4479.2762 0 -4479.2762 1279.8628 Loop time of 1.757e-06 on 1 procs for 0 steps with 690 atoms 170.7% 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 | | 1.757e-06 | | |100.00 Nlocal: 690.000 ave 690 max 690 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4018.00 ave 4018 max 4018 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: 51754.0 ave 51754 max 51754 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 51754 Ave neighs/atom = 75.005797 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 9 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/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) = 5.414 | 5.414 | 5.414 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 -4479.2762 -4479.2762 28.758367 80.870593 4.3491642 1279.8628 1279.8628 56.76299 3713.6237 69.20167 2.5017218 1663.1286 Loop time of 1.693e-06 on 1 procs for 0 steps with 690 atoms 177.2% 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 | | 1.693e-06 | | |100.00 Nlocal: 690.000 ave 690 max 690 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4018.00 ave 4018 max 4018 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 25877.0 ave 25877 max 25877 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 51754.0 ave 51754 max 51754 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 51754 Ave neighs/atom = 75.005797 Neighbor list builds = 0 Dangerous builds = 0 690 -4479.2762025058 eV 2.50172179689362 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:43