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 = 3.6200001 3.6200001 3.6200001 Created orthogonal box = (0.0000000 -42.832418 0.0000000) to (52.458785 42.832418 8.8671530) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9952897 5.5070252 5.9114353 Created 1671 atoms using lattice units in orthogonal box = (0.0000000 -42.832418 0.0000000) to (52.458785 42.832418 8.8671530) create_atoms CPU = 0.003 seconds 1671 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9952897 5.5070252 5.9114353 Created 1695 atoms using lattice units in orthogonal box = (0.0000000 -42.832418 0.0000000) to (52.458785 42.832418 8.8671530) create_atoms CPU = 0.002 seconds 1695 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 14 22 3 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 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 3358 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_803527979660_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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 14 22 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 6.970 | 6.970 | 6.970 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11665.899 0 -11665.899 7034.9654 70 0 -11846.588 0 -11846.588 6568.2162 Loop time of 3.96166 on 1 procs for 70 steps with 3358 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11665.8987252529 -11846.5769739792 -11846.5877264443 Force two-norm initial, final = 94.014852 0.36706890 Force max component initial, final = 8.7072812 0.081956587 Final line search alpha, max atom move = 1.0000000 0.081956587 Iterations, force evaluations = 70 131 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.8783 | 3.8783 | 3.8783 | 0.0 | 97.90 Neigh | 0.039632 | 0.039632 | 0.039632 | 0.0 | 1.00 Comm | 0.018738 | 0.018738 | 0.018738 | 0.0 | 0.47 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02496 | | | 0.63 Nlocal: 3358.00 ave 3358 max 3358 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10772.0 ave 10772 max 10772 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: 582746.0 ave 582746 max 582746 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 582746 Ave neighs/atom = 173.53961 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 14 22 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 70 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.973 | 6.973 | 6.973 Mbytes Step Temp E_pair E_mol TotEng Press Volume 70 0 -11846.588 0 -11846.588 6568.2162 39847.861 78 0 -11847.732 0 -11847.732 -60.023306 40047.366 Loop time of 0.300298 on 1 procs for 8 steps with 3358 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 = -11846.5877264443 -11847.7274693317 -11847.7324158252 Force two-norm initial, final = 349.86460 2.7116961 Force max component initial, final = 329.48904 1.6693526 Final line search alpha, max atom move = 7.2049629e-05 0.00012027623 Iterations, force evaluations = 8 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.29263 | 0.29263 | 0.29263 | 0.0 | 97.45 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00096763 | 0.00096763 | 0.00096763 | 0.0 | 0.32 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006699 | | | 2.23 Nlocal: 3358.00 ave 3358 max 3358 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11060.0 ave 11060 max 11060 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: 583698.0 ave 583698 max 583698 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 583698 Ave neighs/atom = 173.82311 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 14 23 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 7.112 | 7.112 | 7.112 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11847.732 0 -11847.732 -60.023306 Loop time of 2.474e-06 on 1 procs for 0 steps with 3358 atoms 202.1% 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 | | 2.474e-06 | | |100.00 Nlocal: 3358.00 ave 3358 max 3358 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11146.0 ave 11146 max 11146 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: 582970.0 ave 582970 max 582970 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 582970 Ave neighs/atom = 173.60631 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 14 23 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 7.112 | 7.112 | 7.112 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 -11847.732 -11847.732 52.4387 86.306826 8.8486475 -60.023306 -60.023306 -55.532726 -57.89072 -66.646471 2.3231213 1469.8779 Loop time of 2.621e-06 on 1 procs for 0 steps with 3358 atoms 343.4% 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 | | 2.621e-06 | | |100.00 Nlocal: 3358.00 ave 3358 max 3358 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11146.0 ave 11146 max 11146 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 291485.0 ave 291485 max 291485 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 582970.0 ave 582970 max 582970 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 582970 Ave neighs/atom = 173.60631 Neighbor list builds = 0 Dangerous builds = 0 3358 -11847.7324158252 eV 2.32312127535972 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05