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 = 3.6473074 3.6473074 3.6473074 Created orthogonal box = (0.0000000 -45.118348 0.0000000) to (15.038234 45.118348 3.6473074) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.4230099 4.4230099 3.6473074 Created 206 atoms using lattice units in orthogonal box = (0.0000000 -45.118348 0.0000000) to (15.038234 45.118348 3.6473074) create_atoms CPU = 0.002 seconds 206 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.4230099 4.4230099 3.6473074 Created 206 atoms using lattice units in orthogonal box = (0.0000000 -45.118348 0.0000000) to (15.038234 45.118348 3.6473074) create_atoms CPU = 0.001 seconds 206 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 6 34 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 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 8 atoms, new total = 404 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_608695023236_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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 6 34 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 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) = 4.823 | 4.823 | 4.823 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1658.511 0 -1658.511 677.06774 55 0 -1667.5819 0 -1667.5819 -7087.449 Loop time of 6.65 on 1 procs for 55 steps with 404 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 = -1658.51102944198 -1667.58031101727 -1667.58194584159 Force two-norm initial, final = 19.496394 0.15217938 Force max component initial, final = 6.1020338 0.025950242 Final line search alpha, max atom move = 1.0000000 0.025950242 Iterations, force evaluations = 55 106 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.6359 | 6.6359 | 6.6359 | 0.0 | 99.79 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0068753 | 0.0068753 | 0.0068753 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00719 | | | 0.11 Nlocal: 404.000 ave 404 max 404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2342.00 ave 2342 max 2342 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: 21576.0 ave 21576 max 21576 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 21576 Ave neighs/atom = 53.405941 Neighbor list builds = 0 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 6 34 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 55 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.823 | 4.823 | 4.823 Mbytes Step Temp E_pair E_mol TotEng Press Volume 55 0 -1667.5819 0 -1667.5819 -7087.449 4949.398 58 0 -1667.6191 0 -1667.6191 -966.20128 4930.4289 Loop time of 0.271325 on 1 procs for 3 steps with 404 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1667.58194584159 -1667.61765678545 -1667.61909686407 Force two-norm initial, final = 27.455910 3.0574977 Force max component initial, final = 22.552311 3.0021469 Final line search alpha, max atom move = 0.00026257549 0.00078829019 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.27018 | 0.27018 | 0.27018 | 0.0 | 99.58 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00025009 | 0.00025009 | 0.00025009 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.000895 | | | 0.33 Nlocal: 404.000 ave 404 max 404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2293.00 ave 2293 max 2293 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: 21624.0 ave 21624 max 21624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 21624 Ave neighs/atom = 53.524752 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 6 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 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) = 4.961 | 4.961 | 4.961 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1667.6191 0 -1667.6191 -966.20128 Loop time of 5.714e-06 on 1 procs for 0 steps with 404 atoms 175.0% 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 | | 5.714e-06 | | |100.00 Nlocal: 404.000 ave 404 max 404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2297.00 ave 2297 max 2297 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: 21624.0 ave 21624 max 21624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 21624 Ave neighs/atom = 53.524752 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 6 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 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) = 4.961 | 4.961 | 4.961 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 -1667.6191 -1667.6191 14.997189 90.236696 3.6432725 -966.20128 -966.20128 180.13137 -4053.2241 974.48886 2.3382408 84.201154 Loop time of 7.077e-06 on 1 procs for 0 steps with 404 atoms 254.3% 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 | | 7.077e-06 | | |100.00 Nlocal: 404.000 ave 404 max 404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2297.00 ave 2297 max 2297 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 10812.0 ave 10812 max 10812 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 21624.0 ave 21624 max 21624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 21624 Ave neighs/atom = 53.524752 Neighbor list builds = 0 Dangerous builds = 0 404 -1667.61909686407 eV 2.33824076523464 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:07