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 -60.628400 0.0000000) to (30.314200 60.628400 3.5239542) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9158162 4.9158162 3.5239542 Created 592 atoms using lattice units in orthogonal box = (0.0000000 -60.628400 0.0000000) to (30.314200 60.628400 3.5239542) create_atoms CPU = 0.001 seconds 592 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9158162 4.9158162 3.5239542 Created 594 atoms using lattice units in orthogonal box = (0.0000000 -60.628400 0.0000000) to (30.314200 60.628400 3.5239542) create_atoms CPU = 0.001 seconds 594 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 = 8 32 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 7.709524 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 1184 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 = 8 32 1 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) = 5.467 | 5.467 | 5.467 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5052.0203 0 -5052.0203 27387.584 67 0 -5234.0691 0 -5234.0691 5643.6442 Loop time of 1.47673 on 1 procs for 67 steps with 1184 atoms 96.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5052.02026936496 -5234.06435635466 -5234.06907594204 Force two-norm initial, final = 260.48150 0.21427320 Force max component initial, final = 72.649176 0.024625371 Final line search alpha, max atom move = 1.0000000 0.024625371 Iterations, force evaluations = 67 116 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.4413 | 1.4413 | 1.4413 | 0.0 | 97.60 Neigh | 0.013348 | 0.013348 | 0.013348 | 0.0 | 0.90 Comm | 0.012725 | 0.012725 | 0.012725 | 0.0 | 0.86 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009354 | | | 0.63 Nlocal: 1184.00 ave 1184 max 1184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9624.00 ave 9624 max 9624 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: 207792.0 ave 207792 max 207792 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 207792 Ave neighs/atom = 175.50000 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 = 8 32 1 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 : 67 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.460 | 5.460 | 5.460 Mbytes Step Temp E_pair E_mol TotEng Press Volume 67 0 -5234.0691 0 -5234.0691 5643.6442 12953.361 71 0 -5234.2152 0 -5234.2152 349.84003 12991.545 Loop time of 0.0745421 on 1 procs for 4 steps with 1184 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 = -5234.06907594204 -5234.21294730684 -5234.21521747737 Force two-norm initial, final = 94.878722 5.9417130 Force max component initial, final = 86.105110 4.7349574 Final line search alpha, max atom move = 0.00014041424 0.00066485546 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.072032 | 0.072032 | 0.072032 | 0.0 | 96.63 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00042972 | 0.00042972 | 0.00042972 | 0.0 | 0.58 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00208 | | | 2.79 Nlocal: 1184.00 ave 1184 max 1184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8881.00 ave 8881 max 8881 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: 207672.0 ave 207672 max 207672 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 207672 Ave neighs/atom = 175.39865 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 = 8 32 1 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) = 5.598 | 5.598 | 5.598 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5234.2152 0 -5234.2152 349.84003 Loop time of 1.797e-06 on 1 procs for 0 steps with 1184 atoms 111.3% 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 | | 1.797e-06 | | |100.00 Nlocal: 1184.00 ave 1184 max 1184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8881.00 ave 8881 max 8881 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: 207584.0 ave 207584 max 207584 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 207584 Ave neighs/atom = 175.32432 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 = 8 32 1 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) = 5.598 | 5.598 | 5.598 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 -5234.2152 -5234.2152 30.297214 121.64482 3.5250436 349.84003 349.84003 440.67811 585.80509 23.036898 2.2052815 262.58916 Loop time of 2.625e-06 on 1 procs for 0 steps with 1184 atoms 228.6% 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 | | 2.625e-06 | | |100.00 Nlocal: 1184.00 ave 1184 max 1184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8881.00 ave 8881 max 8881 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 103792.0 ave 103792 max 103792 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 207584.0 ave 207584 max 207584 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 207584 Ave neighs/atom = 175.32432 Neighbor list builds = 0 Dangerous builds = 0 1184 -5234.21521747737 eV 2.20528151969807 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01