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 = 3.5673230 3.5673230 3.5673230 Created orthogonal box = (0.0000000 -67.311683 0.0000000) to (33.654058 67.311683 3.5673230) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9157613 4.9157613 3.5673230 Created 714 atoms using lattice units in orthogonal box = (0.0000000 -67.311683 0.0000000) to (33.654058 67.311683 3.5673230) create_atoms CPU = 0.003 seconds 714 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9157613 4.9157613 3.5673230 Created 714 atoms using lattice units in orthogonal box = (0.0000000 -67.311683 0.0000000) to (33.654058 67.311683 3.5673230) create_atoms CPU = 0.002 seconds 714 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 13 49 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 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 20 atoms, new total = 1408 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_058735400462_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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 13 49 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.683 | 4.683 | 4.683 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5908.7836 0 -5908.7836 -4252.1439 87 0 -5937.4361 0 -5937.4361 13107.638 Loop time of 16.5339 on 1 procs for 87 steps with 1408 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 = -5908.78355119907 -5937.43262763194 -5937.43614162651 Force two-norm initial, final = 23.190271 0.22830875 Force max component initial, final = 5.5505896 0.034026230 Final line search alpha, max atom move = 1.0000000 0.034026230 Iterations, force evaluations = 87 163 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 16.478 | 16.478 | 16.478 | 0.0 | 99.66 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.027674 | 0.027674 | 0.027674 | 0.0 | 0.17 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02863 | | | 0.17 Nlocal: 1408.00 ave 1408 max 1408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6692.00 ave 6692 max 6692 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: 75656.0 ave 75656 max 75656 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 75656 Ave neighs/atom = 53.732955 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 13 49 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 87 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.691 | 4.691 | 4.691 Mbytes Step Temp E_pair E_mol TotEng Press Volume 87 0 -5937.4361 0 -5937.4361 13107.638 16162.194 101 0 -5939.3143 0 -5939.3143 4081.2335 16286.228 Loop time of 1.45622 on 1 procs for 14 steps with 1408 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 = -5937.43614162651 -5939.31330036041 -5939.31427691178 Force two-norm initial, final = 329.52376 13.294523 Force max component initial, final = 298.38454 12.289657 Final line search alpha, max atom move = 0.00080971594 0.0099511309 Iterations, force evaluations = 14 15 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.4436 | 1.4436 | 1.4436 | 0.0 | 99.13 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0026 | 0.0026 | 0.0026 | 0.0 | 0.18 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01001 | | | 0.69 Nlocal: 1408.00 ave 1408 max 1408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7693.00 ave 7693 max 7693 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: 80160.0 ave 80160 max 80160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80160 Ave neighs/atom = 56.931818 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 13 49 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.829 | 4.829 | 4.829 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5939.3143 0 -5939.3143 4081.2335 Loop time of 6.435e-06 on 1 procs for 0 steps with 1408 atoms 186.5% 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 | | 6.435e-06 | | |100.00 Nlocal: 1408.00 ave 1408 max 1408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7689.00 ave 7689 max 7689 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: 78956.0 ave 78956 max 78956 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 78956 Ave neighs/atom = 56.076705 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 13 49 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.829 | 4.829 | 4.829 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 -5939.3143 -5939.3143 34.096499 134.62337 3.5480545 4081.2335 4081.2335 380.56701 10660.655 1202.4789 2.271967 464.87133 Loop time of 6.295e-06 on 1 procs for 0 steps with 1408 atoms 285.9% 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 | | 6.295e-06 | | |100.00 Nlocal: 1408.00 ave 1408 max 1408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7689.00 ave 7689 max 7689 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 39478.0 ave 39478 max 39478 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 78956.0 ave 78956 max 78956 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 78956 Ave neighs/atom = 56.076705 Neighbor list builds = 0 Dangerous builds = 0 1408 -5939.31427691178 eV 2.27196698868925 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:18