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 = 3.6580991 3.6580991 3.6580991 Created orthogonal box = (0.0000000 -40.076126 0.0000000) to (8.1797584 40.076126 8.9604763) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9078550 5.3429958 5.9736509 Created 242 atoms using lattice units in orthogonal box = (0.0000000 -40.076126 0.0000000) to (8.1797584 40.076126 8.9604763) create_atoms CPU = 0.001 seconds 242 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9078550 5.3429958 5.9736509 Created 242 atoms using lattice units in orthogonal box = (0.0000000 -40.076126 0.0000000) to (8.1797584 40.076126 8.9604763) create_atoms CPU = 0.000 seconds 242 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 = 3 22 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 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 472 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_634187028437_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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 3 22 3 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) = 4.515 | 4.515 | 4.515 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1821.3773 0 -1821.3773 -4882.0485 219 0 -1837.411 0 -1837.411 -88882.923 Loop time of 1.41113 on 1 procs for 219 steps with 472 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1821.37733322843 -1837.40926607349 -1837.41098113922 Force two-norm initial, final = 8.9189559 0.12575619 Force max component initial, final = 2.8184570 0.010366011 Final line search alpha, max atom move = 1.0000000 0.010366011 Iterations, force evaluations = 219 428 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.3781 | 1.3781 | 1.3781 | 0.0 | 97.66 Neigh | 0.012496 | 0.012496 | 0.012496 | 0.0 | 0.89 Comm | 0.011799 | 0.011799 | 0.011799 | 0.0 | 0.84 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008755 | | | 0.62 Nlocal: 472.000 ave 472 max 472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3582.00 ave 3582 max 3582 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: 63932.0 ave 63932 max 63932 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 63932 Ave neighs/atom = 135.44915 Neighbor list builds = 3 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 = 3 22 3 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 : 219 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.515 | 4.515 | 4.515 Mbytes Step Temp E_pair E_mol TotEng Press Volume 219 0 -1837.411 0 -1837.411 -88882.923 5874.7218 263 0 -1850.7125 0 -1850.7125 0.087071055 5494.4067 Loop time of 0.172175 on 1 procs for 44 steps with 472 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 = -1837.41098113922 -1850.71146033181 -1850.71245838329 Force two-norm initial, final = 531.18823 2.1900045 Force max component initial, final = 390.71933 1.4230143 Final line search alpha, max atom move = 0.00024658147 0.00035088896 Iterations, force evaluations = 44 49 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.16494 | 0.16494 | 0.16494 | 0.0 | 95.80 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0012799 | 0.0012799 | 0.0012799 | 0.0 | 0.74 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005957 | | | 3.46 Nlocal: 472.000 ave 472 max 472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3578.00 ave 3578 max 3578 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: 63820.0 ave 63820 max 63820 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 63820 Ave neighs/atom = 135.21186 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 = 3 22 3 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) = 4.655 | 4.655 | 4.655 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1850.7125 0 -1850.7125 0.087071055 Loop time of 1.668e-06 on 1 procs for 0 steps with 472 atoms 179.9% 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 | | 1.668e-06 | | |100.00 Nlocal: 472.000 ave 472 max 472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3872.00 ave 3872 max 3872 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: 67300.0 ave 67300 max 67300 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 67300 Ave neighs/atom = 142.58475 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 = 3 22 3 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) = 4.655 | 4.655 | 4.655 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 -1850.7125 -1850.7125 7.9070059 80.152253 8.6694792 0.087071055 0.087071055 401.11639 -447.84997 46.994789 2.3325791 1899.9126 Loop time of 1.371e-06 on 1 procs for 0 steps with 472 atoms 218.8% 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 | | 1.371e-06 | | |100.00 Nlocal: 472.000 ave 472 max 472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3872.00 ave 3872 max 3872 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 33650.0 ave 33650 max 33650 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 67300.0 ave 67300 max 67300 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 67300 Ave neighs/atom = 142.58475 Neighbor list builds = 0 Dangerous builds = 0 472 -1783.96145189624 eV 2.3325790961311 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02