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 = 3.5239542 3.5239542 3.5239542 Created orthogonal box = (0.0000000 -51.794862 0.0000000) to (18.311003 51.794862 4.9836238) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.7472971 5.7545931 4.9836238 Created 434 atoms using lattice units in orthogonal box = (0.0000000 -51.794862 0.0000000) to (18.311003 51.794862 4.9836238) create_atoms CPU = 0.001 seconds 434 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.7472971 5.7545931 4.9836238 Created 434 atoms using lattice units in orthogonal box = (0.0000000 -51.794862 0.0000000) to (18.311003 51.794862 4.9836238) create_atoms CPU = 0.001 seconds 434 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 5 27 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 7.709524 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 856 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_036303866285_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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 5 27 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 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) = 5.014 | 5.014 | 5.014 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3760.0733 0 -3760.0733 5796.5605 46 0 -3780.1274 0 -3780.1274 -5640.8919 Loop time of 0.625958 on 1 procs for 46 steps with 856 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3760.07326063622 -3780.12415048126 -3780.12735298205 Force two-norm initial, final = 28.071922 0.18466455 Force max component initial, final = 8.2753048 0.031327091 Final line search alpha, max atom move = 0.87601073 0.027442867 Iterations, force evaluations = 46 82 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.60946 | 0.60946 | 0.60946 | 0.0 | 97.36 Neigh | 0.0090298 | 0.0090298 | 0.0090298 | 0.0 | 1.44 Comm | 0.0043103 | 0.0043103 | 0.0043103 | 0.0 | 0.69 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003157 | | | 0.50 Nlocal: 856.000 ave 856 max 856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6871.00 ave 6871 max 6871 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: 149452.0 ave 149452 max 149452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 149452 Ave neighs/atom = 174.59346 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 5 27 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 46 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.016 | 5.016 | 5.016 Mbytes Step Temp E_pair E_mol TotEng Press Volume 46 0 -3780.1274 0 -3780.1274 -5640.8919 9453.0958 49 0 -3780.1739 0 -3780.1739 -1843.1774 9433.0151 Loop time of 0.0383178 on 1 procs for 3 steps with 856 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 = -3780.12735298206 -3780.17077186123 -3780.17386541533 Force two-norm initial, final = 42.075174 3.4807626 Force max component initial, final = 38.531711 3.1058309 Final line search alpha, max atom move = 0.00012104264 0.00037593798 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.037119 | 0.037119 | 0.037119 | 0.0 | 96.87 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00025206 | 0.00025206 | 0.00025206 | 0.0 | 0.66 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0009465 | | | 2.47 Nlocal: 856.000 ave 856 max 856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6871.00 ave 6871 max 6871 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: 149560.0 ave 149560 max 149560 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 149560 Ave neighs/atom = 174.71963 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 5 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 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) = 5.154 | 5.154 | 5.154 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3780.1739 0 -3780.1739 -1843.1774 Loop time of 1.591e-06 on 1 procs for 0 steps with 856 atoms 125.7% 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 | | 1.591e-06 | | |100.00 Nlocal: 856.000 ave 856 max 856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6871.00 ave 6871 max 6871 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: 149592.0 ave 149592 max 149592 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 149592 Ave neighs/atom = 174.75701 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 5 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 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) = 5.154 | 5.154 | 5.154 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 -3780.1739 -3780.1739 18.268584 103.58972 4.9845845 -1843.1774 -1843.1774 -526.2964 -4738.6865 -264.54942 2.1950258 386.26159 Loop time of 1.661e-06 on 1 procs for 0 steps with 856 atoms 180.6% 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 | | 1.661e-06 | | |100.00 Nlocal: 856.000 ave 856 max 856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6871.00 ave 6871 max 6871 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 74796.0 ave 74796 max 74796 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 149592.0 ave 149592 max 149592 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 149592 Ave neighs/atom = 174.75701 Neighbor list builds = 0 Dangerous builds = 0 856 -3780.17386541533 eV 2.19502580372267 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00