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 = 3.5200000 3.5200000 3.5200000 Created orthogonal box = (0.0000000 -42.681252 0.0000000) to (34.846222 42.681252 8.6222040) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9780318 4.9355201 5.7481360 Created 1183 atoms using lattice units in orthogonal box = (0.0000000 -42.681252 0.0000000) to (34.846222 42.681252 8.6222040) create_atoms CPU = 0.001 seconds 1183 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9780318 4.9355201 5.7481360 Created 1183 atoms using lattice units in orthogonal box = (0.0000000 -42.681252 0.0000000) to (34.846222 42.681252 8.6222040) create_atoms CPU = 0.001 seconds 1183 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 9 21 3 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 47 atoms, new total = 2319 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_103383163946_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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 9 21 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 6.906 | 6.906 | 6.906 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10215.788 0 -10215.788 3197.2171 76 0 -10266.522 0 -10266.522 -13225.403 Loop time of 3.48182 on 1 procs for 76 steps with 2319 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 = -10215.7881630755 -10266.5124901536 -10266.5224033963 Force two-norm initial, final = 62.424179 0.33144634 Force max component initial, final = 9.6371638 0.034936311 Final line search alpha, max atom move = 1.0000000 0.034936311 Iterations, force evaluations = 76 143 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.4212 | 3.4212 | 3.4212 | 0.0 | 98.26 Neigh | 0.029026 | 0.029026 | 0.029026 | 0.0 | 0.83 Comm | 0.014567 | 0.014567 | 0.014567 | 0.0 | 0.42 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01703 | | | 0.49 Nlocal: 2319.00 ave 2319 max 2319 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9761.00 ave 9761 max 9761 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: 517668.0 ave 517668 max 517668 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 517668 Ave neighs/atom = 223.22898 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 9 21 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 76 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.906 | 6.906 | 6.906 Mbytes Step Temp E_pair E_mol TotEng Press Volume 76 0 -10266.522 0 -10266.522 -13225.403 25647.27 80 0 -10266.961 0 -10266.961 -4145.792 25513.568 Loop time of 0.171806 on 1 procs for 4 steps with 2319 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 = -10266.5224033962 -10266.9605460126 -10266.9614060749 Force two-norm initial, final = 236.70325 0.40609475 Force max component initial, final = 169.37201 0.051202544 Final line search alpha, max atom move = 0.00018828371 9.6406051e-06 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.16814 | 0.16814 | 0.16814 | 0.0 | 97.87 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00055051 | 0.00055051 | 0.00055051 | 0.0 | 0.32 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003114 | | | 1.81 Nlocal: 2319.00 ave 2319 max 2319 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9730.00 ave 9730 max 9730 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: 518470.0 ave 518470 max 518470 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 518470 Ave neighs/atom = 223.57482 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 9 21 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 7.044 | 7.044 | 7.044 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10266.961 0 -10266.961 -4145.792 Loop time of 2.355e-06 on 1 procs for 0 steps with 2319 atoms 169.9% 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 | | 2.355e-06 | | |100.00 Nlocal: 2319.00 ave 2319 max 2319 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9746.00 ave 9746 max 9746 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: 518682.0 ave 518682 max 518682 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 518682 Ave neighs/atom = 223.66624 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 9 21 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 7.044 | 7.044 | 7.044 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 -10266.961 -10266.961 34.744276 85.362504 8.6024229 -4145.792 -4145.792 -1.097154 -12433.071 -3.2079914 2.2120055 1355.2948 Loop time of 2.531e-06 on 1 procs for 0 steps with 2319 atoms 237.1% 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 | | 2.531e-06 | | |100.00 Nlocal: 2319.00 ave 2319 max 2319 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9746.00 ave 9746 max 9746 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 259341.0 ave 259341 max 259341 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 518682.0 ave 518682 max 518682 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 518682 Ave neighs/atom = 223.66624 Neighbor list builds = 0 Dangerous builds = 0 2319 -10203.8119833433 eV 2.21200548101875 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04