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 = 3.6148132 3.6148132 3.6148132 Created orthogonal box = (0.0000000 -38.932730 0.0000000) to (19.466365 38.932730 3.6148132) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.6987778 4.6987778 3.6148132 Created 232 atoms using lattice units in orthogonal box = (0.0000000 -38.932730 0.0000000) to (19.466365 38.932730 3.6148132) create_atoms CPU = 0.001 seconds 232 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.6987778 4.6987778 3.6148132 Created 234 atoms using lattice units in orthogonal box = (0.0000000 -38.932730 0.0000000) to (19.466365 38.932730 3.6148132) create_atoms CPU = 0.000 seconds 234 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 = 11.0375 ghost atom cutoff = 11.0375 binsize = 5.51875, bins = 4 15 1 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 11.037500000000001 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 466 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_380822813353_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 = 11.0375 ghost atom cutoff = 11.0375 binsize = 5.51875, bins = 4 15 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.037500000000001 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) = 5.342 | 5.342 | 5.342 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1546.4662 0 -1546.4662 53540.671 57 0 -1641.267 0 -1641.267 12512.6 Loop time of 3.00967 on 1 procs for 57 steps with 466 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 = -1546.46622588942 -1641.26547302302 -1641.26696823043 Force two-norm initial, final = 136.41833 0.11198558 Force max component initial, final = 40.750906 0.023721032 Final line search alpha, max atom move = 1.0000000 0.023721032 Iterations, force evaluations = 57 106 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.9627 | 2.9627 | 2.9627 | 0.0 | 98.44 Neigh | 0.021624 | 0.021624 | 0.021624 | 0.0 | 0.72 Comm | 0.016636 | 0.016636 | 0.016636 | 0.0 | 0.55 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008715 | | | 0.29 Nlocal: 466.000 ave 466 max 466 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8452.00 ave 8452 max 8452 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: 216628.0 ave 216628 max 216628 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 216628 Ave neighs/atom = 464.86695 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 = 11.0375 ghost atom cutoff = 11.0375 binsize = 5.51875, bins = 4 15 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.037500000000001 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 57 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.342 | 5.342 | 5.342 Mbytes Step Temp E_pair E_mol TotEng Press Volume 57 0 -1641.267 0 -1641.267 12512.6 5479.1801 68 0 -1641.5764 0 -1641.5764 -133.8105 5530.636 Loop time of 0.392437 on 1 procs for 11 steps with 466 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 = -1641.26696823043 -1641.57629364081 -1641.57637050532 Force two-norm initial, final = 78.727939 0.90232858 Force max component initial, final = 63.484640 0.63457259 Final line search alpha, max atom move = 0.0016367520 0.0010386379 Iterations, force evaluations = 11 13 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.38347 | 0.38347 | 0.38347 | 0.0 | 97.71 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0018057 | 0.0018057 | 0.0018057 | 0.0 | 0.46 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007165 | | | 1.83 Nlocal: 466.000 ave 466 max 466 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8452.00 ave 8452 max 8452 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: 216208.0 ave 216208 max 216208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 216208 Ave neighs/atom = 463.96567 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 = 11.0375 ghost atom cutoff = 11.0375 binsize = 5.51875, bins = 4 15 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.037500000000001 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) = 5.479 | 5.479 | 5.479 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1641.5764 0 -1641.5764 -133.8105 Loop time of 3.132e-06 on 1 procs for 0 steps with 466 atoms 127.7% 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 | | 3.132e-06 | | |100.00 Nlocal: 466.000 ave 466 max 466 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8452.00 ave 8452 max 8452 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: 213748.0 ave 213748 max 213748 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 213748 Ave neighs/atom = 458.68670 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 = 11.0375 ghost atom cutoff = 11.0375 binsize = 5.51875, bins = 4 15 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.037500000000001 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) = 5.479 | 5.479 | 5.479 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 -1641.5764 -1641.5764 19.441072 78.645732 3.6172599 -133.8105 -133.8105 -70.769807 -146.70717 -183.95451 2.2463672 292.87419 Loop time of 4.029e-06 on 1 procs for 0 steps with 466 atoms 223.4% 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 | | 4.029e-06 | | |100.00 Nlocal: 466.000 ave 466 max 466 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8452.00 ave 8452 max 8452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 106874.0 ave 106874 max 106874 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 213748.0 ave 213748 max 213748 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 213748 Ave neighs/atom = 458.68670 Neighbor list builds = 0 Dangerous builds = 0 466 -1641.57637050532 eV 2.24636717833684 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03