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 = 3.6584036 3.6584036 3.6584036 Created orthogonal box = (0.0000000 -67.457629 0.0000000) to (33.728815 67.457629 3.6584036) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1585246 5.1585246 3.6584036 Created 679 atoms using lattice units in orthogonal box = (0.0000000 -67.457629 0.0000000) to (33.728815 67.457629 3.6584036) create_atoms CPU = 0.002 seconds 679 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1585246 5.1585246 3.6584036 Created 681 atoms using lattice units in orthogonal box = (0.0000000 -67.457629 0.0000000) to (33.728815 67.457629 3.6584036) create_atoms CPU = 0.002 seconds 681 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 10 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 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1360 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_143977152728_005#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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 10 37 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.094 | 5.094 | 5.094 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4443.4328 0 -4443.4328 129545.69 316 0 -5299.2593 0 -5299.2593 -9670.8689 Loop time of 13.4208 on 1 procs for 316 steps with 1360 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 = -4443.43280771842 -5299.25409028426 -5299.2593270842 Force two-norm initial, final = 1778.8514 0.22168824 Force max component initial, final = 705.51090 0.058234754 Final line search alpha, max atom move = 1.0000000 0.058234754 Iterations, force evaluations = 316 595 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 13.073 | 13.073 | 13.073 | 0.0 | 97.41 Neigh | 0.11954 | 0.11954 | 0.11954 | 0.0 | 0.89 Comm | 0.12884 | 0.12884 | 0.12884 | 0.0 | 0.96 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.09902 | | | 0.74 Nlocal: 1360.00 ave 1360 max 1360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9520.00 ave 9520 max 9520 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: 189340.0 ave 189340 max 189340 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 189340 Ave neighs/atom = 139.22059 Neighbor list builds = 5 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 10 37 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 316 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.094 | 5.094 | 5.094 Mbytes Step Temp E_pair E_mol TotEng Press Volume 316 0 -5299.2593 0 -5299.2593 -9670.8689 16647.682 386 0 -5335.9566 0 -5335.9566 577.57253 16421.955 Loop time of 1.91955 on 1 procs for 70 steps with 1360 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 = -5299.25932708421 -5335.95290640614 -5335.95657989565 Force two-norm initial, final = 865.95081 12.546693 Force max component initial, final = 591.79019 8.8041942 Final line search alpha, max atom move = 0.00019863270 0.0017488009 Iterations, force evaluations = 70 74 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.7125 | 1.7125 | 1.7125 | 0.0 | 89.22 Neigh | 0.13253 | 0.13253 | 0.13253 | 0.0 | 6.90 Comm | 0.017973 | 0.017973 | 0.017973 | 0.0 | 0.94 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.05651 | | | 2.94 Nlocal: 1360.00 ave 1360 max 1360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9615.00 ave 9615 max 9615 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: 195122.0 ave 195122 max 195122 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 195122 Ave neighs/atom = 143.47206 Neighbor list builds = 5 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 9 36 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.232 | 5.232 | 5.232 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5335.9566 0 -5335.9566 577.57253 Loop time of 6.485e-06 on 1 procs for 0 steps with 1360 atoms 200.5% 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 | | 6.485e-06 | | |100.00 Nlocal: 1360.00 ave 1360 max 1360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9615.00 ave 9615 max 9615 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: 195154.0 ave 195154 max 195154 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 195154 Ave neighs/atom = 143.49559 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 9 36 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.232 | 5.232 | 5.232 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 -5335.9566 -5335.9566 32.598143 129.64538 3.8857508 577.57253 577.57253 830.16974 694.94244 207.60542 2.2334361 368.70297 Loop time of 7.557e-06 on 1 procs for 0 steps with 1360 atoms 277.9% 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 | | 7.557e-06 | | |100.00 Nlocal: 1360.00 ave 1360 max 1360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9615.00 ave 9615 max 9615 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 97577.0 ave 97577 max 97577 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 195154.0 ave 195154 max 195154 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 195154 Ave neighs/atom = 143.49559 Neighbor list builds = 0 Dangerous builds = 0 1360 -5335.95657989565 eV 2.23343606322526 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:16