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 = 3.6200000 3.6200000 3.6200000 Created orthogonal box = (0.0000000 -42.216091 0.0000000) to (21.108046 42.216091 3.6200000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9665990 4.9665990 3.6200000 Created 271 atoms using lattice units in orthogonal box = (0.0000000 -42.216091 0.0000000) to (21.108046 42.216091 3.6200000) create_atoms CPU = 0.002 seconds 271 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9665990 4.9665990 3.6200000 Created 273 atoms using lattice units in orthogonal box = (0.0000000 -42.216091 0.0000000) to (21.108046 42.216091 3.6200000) create_atoms CPU = 0.001 seconds 273 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 8 29 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 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 544 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_313717476091_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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 8 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.478 | 4.478 | 4.478 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1698.0897 0 -1698.0897 127116.38 32 0 -1916.3713 0 -1916.3713 5756.9287 Loop time of 1.40588 on 1 procs for 32 steps with 544 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1698.08974365948 -1916.36960017858 -1916.37126272544 Force two-norm initial, final = 838.50318 0.47196072 Force max component initial, final = 315.96167 0.18588123 Final line search alpha, max atom move = 1.0000000 0.18588123 Iterations, force evaluations = 32 58 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.3953 | 1.3953 | 1.3953 | 0.0 | 99.25 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0054104 | 0.0054104 | 0.0054104 | 0.0 | 0.38 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005131 | | | 0.36 Nlocal: 544.000 ave 544 max 544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3863.00 ave 3863 max 3863 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: 42330.0 ave 42330 max 42330 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 42330 Ave neighs/atom = 77.812500 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 8 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 32 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.478 | 4.478 | 4.478 Mbytes Step Temp E_pair E_mol TotEng Press Volume 32 0 -1916.3713 0 -1916.3713 5756.9287 6451.5581 39 0 -1916.5103 0 -1916.5103 -285.97236 6480.469 Loop time of 0.233717 on 1 procs for 7 steps with 544 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 = -1916.37126272544 -1916.50981571761 -1916.51025610986 Force two-norm initial, final = 51.476022 2.1599361 Force max component initial, final = 47.809868 1.2448505 Final line search alpha, max atom move = 0.0010749462 0.0013381473 Iterations, force evaluations = 7 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.22998 | 0.22998 | 0.22998 | 0.0 | 98.40 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00083173 | 0.00083173 | 0.00083173 | 0.0 | 0.36 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002907 | | | 1.24 Nlocal: 544.000 ave 544 max 544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3863.00 ave 3863 max 3863 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: 42056.0 ave 42056 max 42056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 42056 Ave neighs/atom = 77.308824 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 8 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.616 | 4.616 | 4.616 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1916.5103 0 -1916.5103 -285.97236 Loop time of 6.335e-06 on 1 procs for 0 steps with 544 atoms 189.4% 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 | | 6.335e-06 | | |100.00 Nlocal: 544.000 ave 544 max 544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3843.00 ave 3843 max 3843 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: 42032.0 ave 42032 max 42032 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 42032 Ave neighs/atom = 77.264706 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 8 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.616 | 4.616 | 4.616 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 -1916.5103 -1916.5103 21.074605 84.946245 3.6199519 -285.97236 -285.97236 -245.08968 -309.64017 -303.18723 2.2650365 278.37401 Loop time of 6.725e-06 on 1 procs for 0 steps with 544 atoms 223.0% 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 | | 6.725e-06 | | |100.00 Nlocal: 544.000 ave 544 max 544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3843.00 ave 3843 max 3843 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 21016.0 ave 21016 max 21016 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 42032.0 ave 42032 max 42032 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 42032 Ave neighs/atom = 77.264706 Neighbor list builds = 0 Dangerous builds = 0 544 -1916.51025610986 eV 2.26503648440615 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02