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 = 3.1666864 3.1666864 3.1666864 Created orthogonal box = (0.0000000 -32.293992 0.0000000) to (27.967417 32.293992 5.4848617) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0197928 4.9683064 5.4848617 Created 312 atoms using lattice units in orthogonal box = (0.0000000 -32.293992 0.0000000) to (27.967417 32.293992 5.4848617) create_atoms CPU = 0.001 seconds 312 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0197928 4.9683064 5.4848617 Created 315 atoms using lattice units in orthogonal box = (0.0000000 -32.293992 0.0000000) to (27.967417 32.293992 5.4848617) create_atoms CPU = 0.001 seconds 315 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 = 6.7012 ghost atom cutoff = 6.7012 binsize = 3.3506, bins = 9 20 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 6.7012 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 1 atoms, new total = 626 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_560387080449_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 = 6.7012 ghost atom cutoff = 6.7012 binsize = 3.3506, bins = 9 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.7012 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) = 4.496 | 4.496 | 4.496 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 109.93352 0 109.93352 35712.525 149 0 41.225544 0 41.225544 28889.111 Loop time of 54.5317 on 1 procs for 149 steps with 626 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 = 109.933523176319 41.2255831758271 41.2255437425489 Force two-norm initial, final = 49.178142 0.022704811 Force max component initial, final = 11.807245 0.0057140614 Final line search alpha, max atom move = 1.0000000 0.0057140614 Iterations, force evaluations = 149 289 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 54.507 | 54.507 | 54.507 | 0.0 | 99.95 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.012533 | 0.012533 | 0.012533 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01259 | | | 0.02 Nlocal: 626.000 ave 626 max 626 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3294.00 ave 3294 max 3294 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: 41142.0 ave 41142 max 41142 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 41142 Ave neighs/atom = 65.722045 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 = 6.7012 ghost atom cutoff = 6.7012 binsize = 3.3506, bins = 9 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.7012 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 149 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.495 | 4.495 | 4.495 Mbytes Step Temp E_pair E_mol TotEng Press Volume 149 0 41.225544 0 41.225544 28889.111 9907.6297 162 0 39.686478 0 39.686478 -72.929087 10017.081 Loop time of 2.99592 on 1 procs for 13 steps with 626 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 = 41.2255437425488 39.6865029550551 39.6864784590499 Force two-norm initial, final = 330.48138 1.0048480 Force max component initial, final = 273.37513 0.56024342 Final line search alpha, max atom move = 0.0012915459 0.00072358009 Iterations, force evaluations = 13 15 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.9934 | 2.9934 | 2.9934 | 0.0 | 99.92 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00042791 | 0.00042791 | 0.00042791 | 0.0 | 0.01 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002103 | | | 0.07 Nlocal: 626.000 ave 626 max 626 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3259.00 ave 3259 max 3259 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: 40888.0 ave 40888 max 40888 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 40888 Ave neighs/atom = 65.316294 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 = 6.7012 ghost atom cutoff = 6.7012 binsize = 3.3506, bins = 9 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.7012 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) = 4.633 | 4.633 | 4.633 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 39.686478 0 39.686478 -72.929087 Loop time of 1.878e-06 on 1 procs for 0 steps with 626 atoms 106.5% 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 | | 1.878e-06 | | |100.00 Nlocal: 626.000 ave 626 max 626 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3259.00 ave 3259 max 3259 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: 40728.0 ave 40728 max 40728 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 40728 Ave neighs/atom = 65.060703 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 = 6.7012 ghost atom cutoff = 6.7012 binsize = 3.3506, bins = 9 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.7012 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) = 4.633 | 4.633 | 4.633 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 39.686478 39.686478 27.980093 65.336578 5.4794333 -72.929087 -72.929087 -42.983295 -86.284826 -89.51914 2.4413055 592.46032 Loop time of 1.7e-06 on 1 procs for 0 steps with 626 atoms 117.6% 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 | | 1.7e-06 | | |100.00 Nlocal: 626.000 ave 626 max 626 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3259.00 ave 3259 max 3259 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 20364.0 ave 20364 max 20364 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 40728.0 ave 40728 max 40728 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 40728 Ave neighs/atom = 65.060703 Neighbor list builds = 0 Dangerous builds = 0 626 -4265.34526845168 eV 2.44130548700998 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:58