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 -42.216092 0.0000000) to (14.925643 42.216092 5.1194532) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.1458528 6.2082489 5.1194532 Created 272 atoms using lattice units in orthogonal box = (0.0000000 -42.216092 0.0000000) to (14.925643 42.216092 5.1194532) create_atoms CPU = 0.001 seconds 272 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.1458528 6.2082489 5.1194532 Created 274 atoms using lattice units in orthogonal box = (0.0000000 -42.216092 0.0000000) to (14.925643 42.216092 5.1194532) create_atoms CPU = 0.001 seconds 274 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 = 4 22 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 0 atoms, new total = 546 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 = 4 22 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) = 4.532 | 4.532 | 4.532 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1878.5467 0 -1878.5467 23146.966 84 0 -1927.3379 0 -1927.3379 8744.7331 Loop time of 0.841247 on 1 procs for 84 steps with 546 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1878.54671297867 -1927.33603856934 -1927.33791537483 Force two-norm initial, final = 111.16837 0.16760763 Force max component initial, final = 43.813140 0.045330927 Final line search alpha, max atom move = 1.0000000 0.045330927 Iterations, force evaluations = 84 157 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.82211 | 0.82211 | 0.82211 | 0.0 | 97.73 Neigh | 0.0067585 | 0.0067585 | 0.0067585 | 0.0 | 0.80 Comm | 0.0071571 | 0.0071571 | 0.0071571 | 0.0 | 0.85 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005216 | | | 0.62 Nlocal: 546.000 ave 546 max 546 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5038.00 ave 5038 max 5038 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: 94776.0 ave 94776 max 94776 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 94776 Ave neighs/atom = 173.58242 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 = 4 22 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) = 4.533 | 4.533 | 4.533 Mbytes Step Temp E_pair E_mol TotEng Press Volume 84 0 -1927.3379 0 -1927.3379 8744.7331 6451.5585 91 0 -1927.5142 0 -1927.5142 -17.093357 6493.1679 Loop time of 0.0501738 on 1 procs for 7 steps with 546 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 = -1927.33791537483 -1927.51401598163 -1927.51417266508 Force two-norm initial, final = 66.737522 0.44266248 Force max component initial, final = 57.283569 0.27992479 Final line search alpha, max atom move = 0.00054409206 0.00015230486 Iterations, force evaluations = 7 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.048292 | 0.048292 | 0.048292 | 0.0 | 96.25 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00036695 | 0.00036695 | 0.00036695 | 0.0 | 0.73 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001514 | | | 3.02 Nlocal: 546.000 ave 546 max 546 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5116.00 ave 5116 max 5116 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: 95060.0 ave 95060 max 95060 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 95060 Ave neighs/atom = 174.10256 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 = 4 22 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) = 4.670 | 4.670 | 4.670 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1927.5142 0 -1927.5142 -17.093357 Loop time of 1.788e-06 on 1 procs for 0 steps with 546 atoms 167.8% 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 | | 1.788e-06 | | |100.00 Nlocal: 546.000 ave 546 max 546 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5092.00 ave 5092 max 5092 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: 94940.0 ave 94940 max 94940 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 94940 Ave neighs/atom = 173.88278 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 = 4 22 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) = 4.670 | 4.670 | 4.670 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 -1927.5142 -1927.5142 14.935626 84.931885 5.1187325 -17.093357 -17.093357 52.976132 -35.195031 -69.061173 2.382652 292.7159 Loop time of 2.282e-06 on 1 procs for 0 steps with 546 atoms 262.9% 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 | | 2.282e-06 | | |100.00 Nlocal: 546.000 ave 546 max 546 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5092.00 ave 5092 max 5092 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 47470.0 ave 47470 max 47470 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 94940.0 ave 94940 max 94940 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 94940 Ave neighs/atom = 173.88278 Neighbor list builds = 0 Dangerous builds = 0 546 -1927.51417266508 eV 2.38265202543469 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01