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 = 2.8700001 2.8700001 2.8700001 Created orthogonal box = (0.0000000 -49.712730 0.0000000) to (20.293965 49.712730 7.0300358) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8705516 4.3081878 4.6866905 Created 602 atoms using lattice units in orthogonal box = (0.0000000 -49.712730 0.0000000) to (20.293965 49.712730 7.0300358) create_atoms CPU = 0.002 seconds 602 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8705516 4.3081878 4.6866905 Created 602 atoms using lattice units in orthogonal box = (0.0000000 -49.712730 0.0000000) to (20.293965 49.712730 7.0300358) create_atoms CPU = 0.002 seconds 602 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 7 33 3 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 6.1615 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 1196 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_024705128470_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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 7 33 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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) = 4.610 | 4.610 | 4.610 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5006.5937 0 -5006.5937 19001.696 81 0 -5095.3898 0 -5095.3898 2612.8495 Loop time of 1.1641 on 1 procs for 81 steps with 1196 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5006.59370827455 -5095.38477290407 -5095.38975244338 Force two-norm initial, final = 99.922916 0.25463613 Force max component initial, final = 24.650109 0.055708564 Final line search alpha, max atom move = 1.0000000 0.055708564 Iterations, force evaluations = 81 147 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1248 | 1.1248 | 1.1248 | 0.0 | 96.63 Neigh | 0.014425 | 0.014425 | 0.014425 | 0.0 | 1.24 Comm | 0.011207 | 0.011207 | 0.011207 | 0.0 | 0.96 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01363 | | | 1.17 Nlocal: 1196.00 ave 1196 max 1196 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4601.00 ave 4601 max 4601 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: 78356.0 ave 78356 max 78356 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 78356 Ave neighs/atom = 65.515050 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 7 33 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 81 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.610 | 4.610 | 4.610 Mbytes Step Temp E_pair E_mol TotEng Press Volume 81 0 -5095.3898 0 -5095.3898 2612.8495 14184.762 83 0 -5095.3983 0 -5095.3983 971.33535 14198.712 Loop time of 0.039857 on 1 procs for 2 steps with 1196 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 = -5095.38975244338 -5095.39831351053 -5095.3983211051 Force two-norm initial, final = 24.603476 0.44863761 Force max component initial, final = 18.453411 0.28794747 Final line search alpha, max atom move = 0.0075767368 0.0021817022 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.037898 | 0.037898 | 0.037898 | 0.0 | 95.08 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00035233 | 0.00035233 | 0.00035233 | 0.0 | 0.88 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001607 | | | 4.03 Nlocal: 1196.00 ave 1196 max 1196 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4594.00 ave 4594 max 4594 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: 78352.0 ave 78352 max 78352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 78352 Ave neighs/atom = 65.511706 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 7 33 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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) = 4.748 | 4.748 | 4.748 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5095.3983 0 -5095.3983 971.33535 Loop time of 3.033e-06 on 1 procs for 0 steps with 1196 atoms 131.9% 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 | | 3.033e-06 | | |100.00 Nlocal: 1196.00 ave 1196 max 1196 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4586.00 ave 4586 max 4586 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: 78316.0 ave 78316 max 78316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 78316 Ave neighs/atom = 65.481605 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 7 33 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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) = 4.748 | 4.748 | 4.748 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 -5095.3983 -5095.3983 20.304972 99.425459 7.0331351 971.33535 971.33535 -32.50949 2920.2747 26.24088 2.2703751 764.91851 Loop time of 3.264e-06 on 1 procs for 0 steps with 1196 atoms 153.2% 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 | | 3.264e-06 | | |100.00 Nlocal: 1196.00 ave 1196 max 1196 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4586.00 ave 4586 max 4586 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 39158.0 ave 39158 max 39158 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 78316.0 ave 78316 max 78316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 78316 Ave neighs/atom = 65.481605 Neighbor list builds = 0 Dangerous builds = 0 1196 -5095.3982015051 eV 2.27037514231003 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01