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 = 3.6336621 3.6336621 3.6336621 Created orthogonal box = (0.0000000 -47.655031 0.0000000) to (33.697196 47.655031 5.1387742) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2692457 6.0954110 5.1387742 Created 687 atoms using lattice units in orthogonal box = (0.0000000 -47.655031 0.0000000) to (33.697196 47.655031 5.1387742) create_atoms CPU = 0.002 seconds 687 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2692457 6.0954110 5.1387742 Created 695 atoms using lattice units in orthogonal box = (0.0000000 -47.655031 0.0000000) to (33.697196 47.655031 5.1387742) create_atoms CPU = 0.002 seconds 695 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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 12 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, cut 5.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1382 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_529419924683_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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 12 34 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.7 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) = 4.662 | 4.662 | 4.662 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5483.4535 0 -5483.4535 23834.875 66 0 -5654.9044 0 -5654.9044 12078.662 Loop time of 76.8815 on 1 procs for 66 steps with 1382 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 = -5483.4535234909 -5654.89906108589 -5654.90439020557 Force two-norm initial, final = 69.286042 0.19056809 Force max component initial, final = 11.336357 0.033027785 Final line search alpha, max atom move = 0.86186718 0.028465564 Iterations, force evaluations = 66 110 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 76.815 | 76.815 | 76.815 | 0.0 | 99.91 Neigh | 0.03902 | 0.03902 | 0.03902 | 0.0 | 0.05 Comm | 0.012591 | 0.012591 | 0.012591 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0151 | | | 0.02 Nlocal: 1382.00 ave 1382 max 1382 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5369.00 ave 5369 max 5369 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: 79586.0 ave 79586 max 79586 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 79586 Ave neighs/atom = 57.587554 Neighbor list builds = 3 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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 12 34 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 66 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.662 | 4.662 | 4.662 Mbytes Step Temp E_pair E_mol TotEng Press Volume 66 0 -5654.9044 0 -5654.9044 12078.662 16504.108 71 0 -5655.4438 0 -5655.4438 -6.533784 16640.169 Loop time of 5.51476 on 1 procs for 5 steps with 1382 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 = -5654.90439020557 -5655.43938337044 -5655.44383737255 Force two-norm initial, final = 217.69638 0.25645464 Force max component initial, final = 141.78560 0.083578252 Final line search alpha, max atom move = 7.0892158e-05 5.9250426e-06 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.5106 | 5.5106 | 5.5106 | 0.0 | 99.93 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00065803 | 0.00065803 | 0.00065803 | 0.0 | 0.01 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003469 | | | 0.06 Nlocal: 1382.00 ave 1382 max 1382 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5365.00 ave 5365 max 5365 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: 80262.0 ave 80262 max 80262 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80262 Ave neighs/atom = 58.076700 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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 12 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.7 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) = 4.800 | 4.800 | 4.800 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5655.4438 0 -5655.4438 -6.533784 Loop time of 3.046e-06 on 1 procs for 0 steps with 1382 atoms 164.1% 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 | | 3.046e-06 | | |100.00 Nlocal: 1382.00 ave 1382 max 1382 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5358.00 ave 5358 max 5358 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: 78474.0 ave 78474 max 78474 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 78474 Ave neighs/atom = 56.782923 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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 12 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.7 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) = 4.800 | 4.800 | 4.800 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 -5655.4438 -5655.4438 33.805565 95.693744 5.1438227 -6.533784 -6.533784 -4.9808243 -8.0796157 -6.5409119 2.4122871 942.65331 Loop time of 3.111e-06 on 1 procs for 0 steps with 1382 atoms 160.7% 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 | | 3.111e-06 | | |100.00 Nlocal: 1382.00 ave 1382 max 1382 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5358.00 ave 5358 max 5358 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 39237.0 ave 39237 max 39237 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 78474.0 ave 78474 max 78474 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 78474 Ave neighs/atom = 56.782923 Neighbor list builds = 0 Dangerous builds = 0 1382 -3533.74904024641 eV 2.4122870881719 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:01:25