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 = 3.5240105 3.5240105 3.5240105 Created orthogonal box = (0.0000000 -55.046804 0.0000000) to (27.523402 55.046804 3.5240105) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9632364 4.9632364 3.5240105 Created 488 atoms using lattice units in orthogonal box = (0.0000000 -55.046804 0.0000000) to (27.523402 55.046804 3.5240105) create_atoms CPU = 0.001 seconds 488 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9632364 4.9632364 3.5240105 Created 490 atoms using lattice units in orthogonal box = (0.0000000 -55.046804 0.0000000) to (27.523402 55.046804 3.5240105) create_atoms CPU = 0.001 seconds 490 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 8 29 1 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 7.65 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 978 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_535504325462_003#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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 8 29 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 5.034 | 5.034 | 5.034 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4329.2126 0 -4329.2126 21221.174 72 0 -4418.4749 0 -4418.4749 9646.2252 Loop time of 1.31097 on 1 procs for 72 steps with 978 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 = -4329.21259993231 -4418.47073229958 -4418.4748867817 Force two-norm initial, final = 62.966254 0.22139516 Force max component initial, final = 9.2076649 0.027221869 Final line search alpha, max atom move = 1.0000000 0.027221869 Iterations, force evaluations = 72 128 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.2778 | 1.2778 | 1.2778 | 0.0 | 97.47 Neigh | 0.011716 | 0.011716 | 0.011716 | 0.0 | 0.89 Comm | 0.012652 | 0.012652 | 0.012652 | 0.0 | 0.97 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008784 | | | 0.67 Nlocal: 978.000 ave 978 max 978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8543.00 ave 8543 max 8543 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: 170972.0 ave 170972 max 170972 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 170972 Ave neighs/atom = 174.81800 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 8 29 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 72 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.034 | 5.034 | 5.034 Mbytes Step Temp E_pair E_mol TotEng Press Volume 72 0 -4418.4749 0 -4418.4749 9646.2252 10678.283 78 0 -4418.8173 0 -4418.8173 307.97397 10732.886 Loop time of 0.0793475 on 1 procs for 6 steps with 978 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 = -4418.4748867817 -4418.81412784395 -4418.81729312344 Force two-norm initial, final = 134.63098 4.8452246 Force max component initial, final = 122.10629 4.2415425 Final line search alpha, max atom move = 0.00016075263 0.00068183910 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.076264 | 0.076264 | 0.076264 | 0.0 | 96.11 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00056206 | 0.00056206 | 0.00056206 | 0.0 | 0.71 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002521 | | | 3.18 Nlocal: 978.000 ave 978 max 978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8537.00 ave 8537 max 8537 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: 171112.0 ave 171112 max 171112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 171112 Ave neighs/atom = 174.96115 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 8 29 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 5.172 | 5.172 | 5.172 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4418.8173 0 -4418.8173 307.97397 Loop time of 1.702e-06 on 1 procs for 0 steps with 978 atoms 176.3% 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 | | 1.702e-06 | | |100.00 Nlocal: 978.000 ave 978 max 978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8543.00 ave 8543 max 8543 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: 170888.0 ave 170888 max 170888 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 170888 Ave neighs/atom = 174.73211 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 8 29 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 5.172 | 5.172 | 5.172 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 -4418.8173 -4418.8173 27.497729 110.69286 3.5261443 307.97397 307.97397 632.57552 345.17784 -53.831441 2.2381966 149.56614 Loop time of 2.329e-06 on 1 procs for 0 steps with 978 atoms 257.6% 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 | | 2.329e-06 | | |100.00 Nlocal: 978.000 ave 978 max 978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8543.00 ave 8543 max 8543 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 85444.0 ave 85444 max 85444 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 170888.0 ave 170888 max 170888 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 170888 Ave neighs/atom = 174.73211 Neighbor list builds = 0 Dangerous builds = 0 978 -4418.81729312344 eV 2.23819663891481 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01