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 = 3.6133156 3.6133156 3.6133156 Created orthogonal box = (0.0000000 -69.130412 0.0000000) to (39.910376 69.130412 6.2584463) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8884161 5.2883890 6.2584463 Created 1466 atoms using lattice units in orthogonal box = (0.0000000 -69.130412 0.0000000) to (39.910376 69.130412 6.2584463) create_atoms CPU = 0.008 seconds 1466 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8884161 5.2883890 6.2584463 Created 1466 atoms using lattice units in orthogonal box = (0.0000000 -69.130412 0.0000000) to (39.910376 69.130412 6.2584463) create_atoms CPU = 0.007 seconds 1466 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 12 41 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 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 32 atoms, new total = 2900 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_486450342170_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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 12 41 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 6.187 | 6.187 | 6.187 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10193.341 0 -10193.341 1371.6706 71 0 -10234.537 0 -10234.537 -8387.7186 Loop time of 23.5715 on 1 procs for 71 steps with 2900 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 = -10193.3409325316 -10234.5295185665 -10234.5374390575 Force two-norm initial, final = 46.646715 0.29564581 Force max component initial, final = 10.137112 0.082482969 Final line search alpha, max atom move = 1.0000000 0.082482969 Iterations, force evaluations = 71 121 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 23.42 | 23.42 | 23.42 | 0.0 | 99.36 Neigh | 0.089198 | 0.089198 | 0.089198 | 0.0 | 0.38 Comm | 0.026454 | 0.026454 | 0.026454 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03585 | | | 0.15 Nlocal: 2900.00 ave 2900 max 2900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9901.00 ave 9901 max 9901 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: 372104.0 ave 372104 max 372104 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 372104 Ave neighs/atom = 128.31172 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 12 41 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 71 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.187 | 6.187 | 6.187 Mbytes Step Temp E_pair E_mol TotEng Press Volume 71 0 -10234.537 0 -10234.537 -8387.7186 34534.366 74 0 -10234.791 0 -10234.791 -3022.8854 34401.289 Loop time of 0.966366 on 1 procs for 3 steps with 2900 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 = -10234.5374390575 -10234.7850692852 -10234.7914399191 Force two-norm initial, final = 183.98595 9.4801966 Force max component initial, final = 147.94269 9.4701906 Final line search alpha, max atom move = 3.9517427e-05 0.00037423757 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.96117 | 0.96117 | 0.96117 | 0.0 | 99.46 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00099263 | 0.00099263 | 0.00099263 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004203 | | | 0.43 Nlocal: 2900.00 ave 2900 max 2900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9898.00 ave 9898 max 9898 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: 372276.0 ave 372276 max 372276 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 372276 Ave neighs/atom = 128.37103 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 12 41 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 6.325 | 6.325 | 6.325 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10234.791 0 -10234.791 -3022.8854 Loop time of 6.014e-06 on 1 procs for 0 steps with 2900 atoms 199.5% 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 | | 6.014e-06 | | |100.00 Nlocal: 2900.00 ave 2900 max 2900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9913.00 ave 9913 max 9913 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: 374212.0 ave 374212 max 374212 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 374212 Ave neighs/atom = 129.03862 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 12 41 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 6.325 | 6.325 | 6.325 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 -10234.791 -10234.791 39.810533 138.26082 6.2499649 -3022.8854 -3022.8854 -13.89252 -9495.2226 440.45892 2.305098 1069.4815 Loop time of 6.435e-06 on 1 procs for 0 steps with 2900 atoms 357.4% 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 | | 6.435e-06 | | |100.00 Nlocal: 2900.00 ave 2900 max 2900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9913.00 ave 9913 max 9913 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 187106.0 ave 187106 max 187106 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 374212.0 ave 374212 max 374212 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 374212 Ave neighs/atom = 129.03862 Neighbor list builds = 0 Dangerous builds = 0 2900 -10234.7914399191 eV 2.30509796233464 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:26