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 = 4.0397985 4.0397985 4.0397985 Created orthogonal box = (0.0000000 -48.477581 0.0000000) to (17.139413 48.477581 5.7131378) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7131378 6.7329974 5.7131378 Created 288 atoms using lattice units in orthogonal box = (0.0000000 -48.477581 0.0000000) to (17.139413 48.477581 5.7131378) create_atoms CPU = 0.001 seconds 288 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7131378 6.7329974 5.7131378 Created 292 atoms using lattice units in orthogonal box = (0.0000000 -48.477581 0.0000000) to (17.139413 48.477581 5.7131378) create_atoms CPU = 0.001 seconds 292 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 = 11.77941 ghost atom cutoff = 11.77941 binsize = 5.889705, bins = 3 17 1 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 11.77941 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 572 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_279544746097_004#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 = 11.77941 ghost atom cutoff = 11.77941 binsize = 5.889705, bins = 3 17 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.77941 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) = 5.397 | 5.397 | 5.397 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1617.5717 0 -1617.5717 6055.8022 63 0 -1641.0497 0 -1641.0497 -1907.3459 Loop time of 1.25386 on 1 procs for 63 steps with 572 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 = -1617.57172288569 -1641.04841260156 -1641.04974723022 Force two-norm initial, final = 31.304236 0.11089346 Force max component initial, final = 6.7777804 0.013796654 Final line search alpha, max atom move = 1.0000000 0.013796654 Iterations, force evaluations = 63 122 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.2274 | 1.2274 | 1.2274 | 0.0 | 97.89 Neigh | 0.013723 | 0.013723 | 0.013723 | 0.0 | 1.09 Comm | 0.0079545 | 0.0079545 | 0.0079545 | 0.0 | 0.63 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004756 | | | 0.38 Nlocal: 572.000 ave 572 max 572 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7942.00 ave 7942 max 7942 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: 230824.0 ave 230824 max 230824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 230824 Ave neighs/atom = 403.53846 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 = 11.77941 ghost atom cutoff = 11.77941 binsize = 5.889705, bins = 3 17 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.77941 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 63 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.397 | 5.397 | 5.397 Mbytes Step Temp E_pair E_mol TotEng Press Volume 63 0 -1641.0497 0 -1641.0497 -1907.3459 9493.833 69 0 -1641.1122 0 -1641.1122 -29.094174 9469.81 Loop time of 0.0801668 on 1 procs for 6 steps with 572 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 = -1641.04974723022 -1641.11220202467 -1641.11224337332 Force two-norm initial, final = 26.839938 0.48403721 Force max component initial, final = 25.982948 0.43796869 Final line search alpha, max atom move = 0.0015547480 0.00068093093 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.077899 | 0.077899 | 0.077899 | 0.0 | 97.17 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00045391 | 0.00045391 | 0.00045391 | 0.0 | 0.57 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001814 | | | 2.26 Nlocal: 572.000 ave 572 max 572 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7956.00 ave 7956 max 7956 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: 230480.0 ave 230480 max 230480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 230480 Ave neighs/atom = 402.93706 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 = 11.77941 ghost atom cutoff = 11.77941 binsize = 5.889705, bins = 3 17 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.77941 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) = 5.535 | 5.535 | 5.535 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1641.1122 0 -1641.1122 -29.094174 Loop time of 2.016e-06 on 1 procs for 0 steps with 572 atoms 148.8% 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 | | 2.016e-06 | | |100.00 Nlocal: 572.000 ave 572 max 572 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7931.00 ave 7931 max 7931 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: 232528.0 ave 232528 max 232528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 232528 Ave neighs/atom = 406.51748 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 = 11.77941 ghost atom cutoff = 11.77941 binsize = 5.889705, bins = 3 17 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.77941 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) = 5.535 | 5.535 | 5.535 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 -1641.1122 -1641.1122 17.053686 97.027045 5.7230851 -29.094174 -29.094174 -73.728342 -10.181052 -3.3731281 2.6195899 479.60522 Loop time of 2.611e-06 on 1 procs for 0 steps with 572 atoms 229.8% 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 | | 2.611e-06 | | |100.00 Nlocal: 572.000 ave 572 max 572 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7931.00 ave 7931 max 7931 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 116264.0 ave 116264 max 116264 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 232528.0 ave 232528 max 232528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 232528 Ave neighs/atom = 406.51748 Neighbor list builds = 0 Dangerous builds = 0 572 -1641.11224337332 eV 2.61958994019085 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01