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 -55.582459 0.0000000) to (32.088731 55.582459 5.4500000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9367279 4.9878870 5.4500000 Created 628 atoms using lattice units in orthogonal box = (0.0000000 -55.582459 0.0000000) to (32.088731 55.582459 5.4500000) create_atoms CPU = 0.005 seconds 628 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9367279 4.9878870 5.4500000 Created 627 atoms using lattice units in orthogonal box = (0.0000000 -55.582459 0.0000000) to (32.088731 55.582459 5.4500000) create_atoms CPU = 0.004 seconds 627 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 9 28 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 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 7 atoms, new total = 1248 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_380272712420_001#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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 9 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 5.063 | 5.063 | 5.063 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8011.094 0 -8011.094 108229.15 28 0 -8457.7867 0 -8457.7867 8132.8102 Loop time of 11.1559 on 1 procs for 28 steps with 1248 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 = -8011.094029895 -8457.77895329821 -8457.78672066838 Force two-norm initial, final = 439.32002 0.50949289 Force max component initial, final = 75.655149 0.093943649 Final line search alpha, max atom move = 1.0000000 0.093943649 Iterations, force evaluations = 28 50 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 11.138 | 11.138 | 11.138 | 0.0 | 99.84 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0093826 | 0.0093826 | 0.0093826 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00878 | | | 0.08 Nlocal: 1248.00 ave 1248 max 1248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7208.00 ave 7208 max 7208 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: 169740.0 ave 169740 max 169740 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 169740 Ave neighs/atom = 136.00962 Neighbor list builds = 0 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 9 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 28 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.063 | 5.063 | 5.063 Mbytes Step Temp E_pair E_mol TotEng Press Volume 28 0 -8457.7867 0 -8457.7867 8132.8102 19440.919 30 0 -8457.864 0 -8457.864 2621.6836 19481.382 Loop time of 0.791193 on 1 procs for 2 steps with 1248 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 = -8457.78672066839 -8457.86241022322 -8457.86396349053 Force two-norm initial, final = 106.16581 5.2537798 Force max component initial, final = 82.305020 5.1857191 Final line search alpha, max atom move = 7.6320518e-05 0.00039577677 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.78863 | 0.78863 | 0.78863 | 0.0 | 99.68 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00060048 | 0.00060048 | 0.00060048 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001963 | | | 0.25 Nlocal: 1248.00 ave 1248 max 1248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7256.00 ave 7256 max 7256 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: 169826.0 ave 169826 max 169826 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 169826 Ave neighs/atom = 136.07853 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 9 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 5.201 | 5.201 | 5.201 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8457.864 0 -8457.864 2621.6836 Loop time of 8.299e-06 on 1 procs for 0 steps with 1248 atoms 518.1% 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 | | 8.299e-06 | | |100.00 Nlocal: 1248.00 ave 1248 max 1248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7256.00 ave 7256 max 7256 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: 169782.0 ave 169782 max 169782 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 169782 Ave neighs/atom = 136.04327 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 9 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 5.201 | 5.201 | 5.201 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 -8457.864 -8457.864 32.115923 111.16492 5.4567192 2621.6836 2621.6836 -426.84229 8236.6534 55.239736 2.5123793 775.81693 Loop time of 7.167e-06 on 1 procs for 0 steps with 1248 atoms 279.1% 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 | | 7.167e-06 | | |100.00 Nlocal: 1248.00 ave 1248 max 1248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7256.00 ave 7256 max 7256 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 84891.0 ave 84891 max 84891 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 169782.0 ave 169782 max 169782 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 169782 Ave neighs/atom = 136.04327 Neighbor list builds = 0 Dangerous builds = 0 1248 -8457.86396349053 eV 2.51237925421148 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:13