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 = 2.8886457 2.8886457 2.8886457 Created orthogonal box = (0.0000000 -51.026544 0.0000000) to (29.458521 51.026544 5.0032811) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.5320802 4.5790460 5.0032811 Created 627 atoms using lattice units in orthogonal box = (0.0000000 -51.026544 0.0000000) to (29.458521 51.026544 5.0032811) create_atoms CPU = 0.002 seconds 627 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.5320802 4.5790460 5.0032811 Created 627 atoms using lattice units in orthogonal box = (0.0000000 -51.026544 0.0000000) to (29.458521 51.026544 5.0032811) create_atoms CPU = 0.001 seconds 627 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 12 39 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, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 6 atoms, new total = 1248 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_608695023236_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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 12 39 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 5.395 | 5.395 | 5.395 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5059.726 0 -5059.726 33015.741 40 0 -5190.8479 0 -5190.8479 3903.0144 Loop time of 6.6233 on 1 procs for 40 steps with 1248 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 = -5059.72601564002 -5190.84375018848 -5190.84787715497 Force two-norm initial, final = 160.70178 0.25170459 Force max component initial, final = 26.653338 0.044494854 Final line search alpha, max atom move = 1.0000000 0.044494854 Iterations, force evaluations = 40 73 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.5965 | 6.5965 | 6.5965 | 0.0 | 99.60 Neigh | 0.019463 | 0.019463 | 0.019463 | 0.0 | 0.29 Comm | 0.0029794 | 0.0029794 | 0.0029794 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004335 | | | 0.07 Nlocal: 1248.00 ave 1248 max 1248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4418.00 ave 4418 max 4418 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: 71900.0 ave 71900 max 71900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 71900 Ave neighs/atom = 57.612179 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 12 39 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 40 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.395 | 5.395 | 5.395 Mbytes Step Temp E_pair E_mol TotEng Press Volume 40 0 -5190.8479 0 -5190.8479 3903.0144 15041.529 42 0 -5190.8668 0 -5190.8668 2569.6725 15052.754 Loop time of 0.355836 on 1 procs for 2 steps with 1248 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 = -5190.84787715497 -5190.8653356105 -5190.86676104743 Force two-norm initial, final = 33.789451 1.2957606 Force max component initial, final = 33.784981 1.2336524 Final line search alpha, max atom move = 0.00011464404 0.00014143090 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.35494 | 0.35494 | 0.35494 | 0.0 | 99.75 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00013322 | 0.00013322 | 0.00013322 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0007678 | | | 0.22 Nlocal: 1248.00 ave 1248 max 1248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4439.00 ave 4439 max 4439 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: 71912.0 ave 71912 max 71912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 71912 Ave neighs/atom = 57.621795 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 12 39 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 5.533 | 5.533 | 5.533 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5190.8668 0 -5190.8668 2569.6725 Loop time of 1.883e-06 on 1 procs for 0 steps with 1248 atoms 159.3% 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 | | 1.883e-06 | | |100.00 Nlocal: 1248.00 ave 1248 max 1248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4437.00 ave 4437 max 4437 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: 71904.0 ave 71904 max 71904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 71904 Ave neighs/atom = 57.615385 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 12 39 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 5.533 | 5.533 | 5.533 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 -5190.8668 -5190.8668 29.448754 102.05309 5.0086754 2569.6725 2569.6725 31.559673 7546.0094 131.44836 2.3070577 706.35765 Loop time of 1.909e-06 on 1 procs for 0 steps with 1248 atoms 157.2% 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 | | 1.909e-06 | | |100.00 Nlocal: 1248.00 ave 1248 max 1248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4437.00 ave 4437 max 4437 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 35952.0 ave 35952 max 35952 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 71904.0 ave 71904 max 71904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 71904 Ave neighs/atom = 57.615385 Neighbor list builds = 0 Dangerous builds = 0 1248 -5190.86676104743 eV 2.30705765984377 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:07