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 = 3.5200010 3.5200010 3.5200010 Created orthogonal box = (0.0000000 -37.583326 0.0000000) to (21.698743 37.583326 6.0968206) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7101956 5.2748528 6.0968206 Created 456 atoms using lattice units in orthogonal box = (0.0000000 -37.583326 0.0000000) to (21.698743 37.583326 6.0968206) create_atoms CPU = 0.003 seconds 456 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7101956 5.2748528 6.0968206 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -37.583326 0.0000000) to (21.698743 37.583326 6.0968206) create_atoms CPU = 0.002 seconds 458 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 6 20 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 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 912 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_469343973171_005#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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 6 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 5.001 | 5.001 | 5.001 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3793.581 0 -3793.581 87622.544 83 0 -4037.5469 0 -4037.5469 15825.235 Loop time of 2.8698 on 1 procs for 83 steps with 912 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 = -3793.5810214618 -4037.54290565678 -4037.54685052266 Force two-norm initial, final = 413.75090 0.25902862 Force max component initial, final = 119.50739 0.049309610 Final line search alpha, max atom move = 1.0000000 0.049309610 Iterations, force evaluations = 83 158 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.7866 | 2.7866 | 2.7866 | 0.0 | 97.10 Neigh | 0.043329 | 0.043329 | 0.043329 | 0.0 | 1.51 Comm | 0.021011 | 0.021011 | 0.021011 | 0.0 | 0.73 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01887 | | | 0.66 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5287.00 ave 5287 max 5287 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: 158344.0 ave 158344 max 158344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 158344 Ave neighs/atom = 173.62281 Neighbor list builds = 2 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 6 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 83 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.001 | 5.001 | 5.001 Mbytes Step Temp E_pair E_mol TotEng Press Volume 83 0 -4037.5469 0 -4037.5469 15825.235 9944.0479 92 0 -4038.233 0 -4038.233 -63.021163 10030.848 Loop time of 0.219182 on 1 procs for 9 steps with 912 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 = -4037.54685052267 -4038.23283188731 -4038.23297903313 Force two-norm initial, final = 190.74072 1.0963420 Force max component initial, final = 167.88017 0.83238293 Final line search alpha, max atom move = 0.00045763555 0.00038092802 Iterations, force evaluations = 9 11 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.21268 | 0.21268 | 0.21268 | 0.0 | 97.03 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.001436 | 0.001436 | 0.001436 | 0.0 | 0.66 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00507 | | | 2.31 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5304.00 ave 5304 max 5304 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: 158364.0 ave 158364 max 158364 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 158364 Ave neighs/atom = 173.64474 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 6 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 5.139 | 5.139 | 5.139 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4038.233 0 -4038.233 -63.021163 Loop time of 6.666e-06 on 1 procs for 0 steps with 912 atoms 180.0% 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 | | 6.666e-06 | | |100.00 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5292.00 ave 5292 max 5292 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: 157972.0 ave 157972 max 157972 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 157972 Ave neighs/atom = 173.21491 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 6 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 5.139 | 5.139 | 5.139 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 -4038.233 -4038.233 21.710484 75.771331 6.0976604 -63.021163 -63.021163 -133.02424 -77.309144 21.269897 2.2934106 545.47359 Loop time of 6.775e-06 on 1 procs for 0 steps with 912 atoms 236.2% 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 | | 6.775e-06 | | |100.00 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5292.00 ave 5292 max 5292 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 78986.0 ave 78986 max 78986 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 157972.0 ave 157972 max 157972 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 157972 Ave neighs/atom = 173.21491 Neighbor list builds = 0 Dangerous builds = 0 912 -4004.98855753743 eV 2.29341061602931 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03