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 = 3.5600001 3.5600001 3.5600001 Created orthogonal box = (0.0000000 -71.381340 0.0000000) to (41.209981 71.381340 6.1661011) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5356691 5.6818134 6.1661011 Created 1610 atoms using lattice units in orthogonal box = (0.0000000 -71.381340 0.0000000) to (41.209981 71.381340 6.1661011) create_atoms CPU = 0.004 seconds 1610 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5356691 5.6818134 6.1661011 Created 1610 atoms using lattice units in orthogonal box = (0.0000000 -71.381340 0.0000000) to (41.209981 71.381340 6.1661011) create_atoms CPU = 0.004 seconds 1610 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 = 11 37 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 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 30 atoms, new total = 3190 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_657255834688_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 = 11 37 2 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) = 10.95 | 10.95 | 10.95 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13906.98 0 -13906.98 -3509.3927 84 0 -13992.217 0 -13992.217 -3498.6498 Loop time of 4.61696 on 1 procs for 84 steps with 3190 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -13906.9802870048 -13992.2038764059 -13992.2174896686 Force two-norm initial, final = 50.933211 0.63571372 Force max component initial, final = 10.879603 0.18235758 Final line search alpha, max atom move = 0.83453960 0.15218462 Iterations, force evaluations = 84 158 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.4336 | 4.4336 | 4.4336 | 0.0 | 96.03 Neigh | 0.10322 | 0.10322 | 0.10322 | 0.0 | 2.24 Comm | 0.043839 | 0.043839 | 0.043839 | 0.0 | 0.95 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03636 | | | 0.79 Nlocal: 3190.00 ave 3190 max 3190 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14460.0 ave 14460 max 14460 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: 558492.0 ave 558492 max 558492 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 558492 Ave neighs/atom = 175.07586 Neighbor list builds = 3 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 = 11 37 2 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 : 84 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 10.95 | 10.95 | 10.95 Mbytes Step Temp E_pair E_mol TotEng Press Volume 84 0 -13992.217 0 -13992.217 -3498.6498 36276.698 86 0 -13992.325 0 -13992.325 478.2015 36199.981 Loop time of 0.11199 on 1 procs for 2 steps with 3190 atoms 98.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -13992.2174896686 -13992.316040043 -13992.3245174568 Force two-norm initial, final = 137.26254 14.300535 Force max component initial, final = 117.67071 14.221461 Final line search alpha, max atom move = 2.8822087e-05 0.00040989218 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.10907 | 0.10907 | 0.10907 | 0.0 | 97.39 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00047861 | 0.00047861 | 0.00047861 | 0.0 | 0.43 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002445 | | | 2.18 Nlocal: 3190.00 ave 3190 max 3190 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14436.0 ave 14436 max 14436 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: 558488.0 ave 558488 max 558488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 558488 Ave neighs/atom = 175.07461 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 = 11 37 2 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) = 10.47 | 10.47 | 10.47 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13992.325 0 -13992.325 478.2015 Loop time of 2.175e-06 on 1 procs for 0 steps with 3190 atoms 183.9% 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 | | 2.175e-06 | | |100.00 Nlocal: 3190.00 ave 3190 max 3190 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14453.0 ave 14453 max 14453 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: 558640.0 ave 558640 max 558640 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 558640 Ave neighs/atom = 175.12226 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 = 11 37 2 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) = 10.47 | 10.47 | 10.47 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 -13992.325 -13992.325 41.148979 142.76268 6.1621828 478.2015 478.2015 -58.970657 864.54687 629.02828 2.3190084 1195.3483 Loop time of 2.19e-06 on 1 procs for 0 steps with 3190 atoms 274.0% 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 | | 2.19e-06 | | |100.00 Nlocal: 3190.00 ave 3190 max 3190 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14453.0 ave 14453 max 14453 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 279320.0 ave 279320 max 279320 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 558640.0 ave 558640 max 558640 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 558640 Ave neighs/atom = 175.12226 Neighbor list builds = 0 Dangerous builds = 0 3190 -13992.3245174568 eV 2.31900843968253 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05