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 = 3.1465590 3.1465590 3.1465590 Created orthogonal box = (0.0000000 -44.944998 0.0000000) to (31.778688 44.944998 4.4499063) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9848922 3.9654575 4.4499063 Created 409 atoms using lattice units in orthogonal box = (0.0000000 -44.944998 0.0000000) to (31.778688 44.944998 4.4499063) create_atoms CPU = 0.003 seconds 409 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9848922 3.9654575 4.4499063 Created 409 atoms using lattice units in orthogonal box = (0.0000000 -44.944998 0.0000000) to (31.778688 44.944998 4.4499063) create_atoms CPU = 0.002 seconds 409 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 11 31 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 5.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 812 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_805823015127_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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 11 31 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.524 | 4.524 | 4.524 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5436.7307 0 -5436.7307 14904.754 59 0 -5498.4613 0 -5498.4613 -2625.9319 Loop time of 4.74697 on 1 procs for 59 steps with 812 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 = -5436.73067492401 -5498.4564474768 -5498.46127855111 Force two-norm initial, final = 36.564499 0.22685082 Force max component initial, final = 8.1645324 0.021985322 Final line search alpha, max atom move = 1.0000000 0.021985322 Iterations, force evaluations = 59 98 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.7168 | 4.7168 | 4.7168 | 0.0 | 99.36 Neigh | 0.0093542 | 0.0093542 | 0.0093542 | 0.0 | 0.20 Comm | 0.0095598 | 0.0095598 | 0.0095598 | 0.0 | 0.20 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01127 | | | 0.24 Nlocal: 812.000 ave 812 max 812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3571.00 ave 3571 max 3571 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: 46600.0 ave 46600 max 46600 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 46600 Ave neighs/atom = 57.389163 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 11 31 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 59 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.524 | 4.524 | 4.524 Mbytes Step Temp E_pair E_mol TotEng Press Volume 59 0 -5498.4613 0 -5498.4613 -2625.9319 12711.541 60 0 -5498.4634 0 -5498.4634 -1829.5933 12707.675 Loop time of 0.138854 on 1 procs for 1 steps with 812 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5498.46127855111 -5498.46127855111 -5498.46340380807 Force two-norm initial, final = 10.370168 5.8243028 Force max component initial, final = 10.090476 5.6672874 Final line search alpha, max atom move = 9.9103350e-05 0.00056164717 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.13773 | 0.13773 | 0.13773 | 0.0 | 99.19 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00028107 | 0.00028107 | 0.00028107 | 0.0 | 0.20 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0008468 | | | 0.61 Nlocal: 812.000 ave 812 max 812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3564.00 ave 3564 max 3564 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: 46686.0 ave 46686 max 46686 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 46686 Ave neighs/atom = 57.495074 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 11 31 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.662 | 4.662 | 4.662 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5498.4634 0 -5498.4634 -1829.5933 Loop time of 6.405e-06 on 1 procs for 0 steps with 812 atoms 171.7% 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 | | 6.405e-06 | | |100.00 Nlocal: 812.000 ave 812 max 812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3564.00 ave 3564 max 3564 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: 46686.0 ave 46686 max 46686 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 46686 Ave neighs/atom = 57.495074 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 11 31 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.662 | 4.662 | 4.662 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 -5498.4634 -5498.4634 31.766041 89.889995 4.4503243 -1829.5933 -1829.5933 166.84797 -6370.2233 714.5955 2.1700496 563.22507 Loop time of 6.916e-06 on 1 procs for 0 steps with 812 atoms 274.7% 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 | | 6.916e-06 | | |100.00 Nlocal: 812.000 ave 812 max 812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3564.00 ave 3564 max 3564 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 23343.0 ave 23343 max 23343 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 46686.0 ave 46686 max 46686 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 46686 Ave neighs/atom = 57.495074 Neighbor list builds = 0 Dangerous builds = 0 812 -5498.46340380807 eV 2.17004960489497 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05