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 = 3.6473074 3.6473074 3.6473074 Created orthogonal box = (0.0000000 -37.195383 0.0000000) to (18.597692 37.195383 3.6473074) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.2917750 4.2917750 3.6473074 Created 208 atoms using lattice units in orthogonal box = (0.0000000 -37.195383 0.0000000) to (18.597692 37.195383 3.6473074) create_atoms CPU = 0.002 seconds 208 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.2917750 4.2917750 3.6473074 Created 210 atoms using lattice units in orthogonal box = (0.0000000 -37.195383 0.0000000) to (18.597692 37.195383 3.6473074) create_atoms CPU = 0.001 seconds 210 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 = 7 28 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 2 atoms, new total = 416 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 = 7 28 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) = 4.815 | 4.815 | 4.815 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1532.1114 0 -1532.1114 99108.958 67 0 -1716.5189 0 -1716.5189 8858.2531 Loop time of 7.29522 on 1 procs for 67 steps with 416 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 = -1532.11144784725 -1716.51750547646 -1716.51885241281 Force two-norm initial, final = 467.46328 0.15123657 Force max component initial, final = 129.19795 0.018311975 Final line search alpha, max atom move = 1.0000000 0.018311975 Iterations, force evaluations = 67 129 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.279 | 7.279 | 7.279 | 0.0 | 99.78 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0082159 | 0.0082159 | 0.0082159 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008018 | | | 0.11 Nlocal: 416.000 ave 416 max 416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2540.00 ave 2540 max 2540 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: 22400.0 ave 22400 max 22400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 22400 Ave neighs/atom = 53.846154 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 7 28 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 : 67 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.815 | 4.815 | 4.815 Mbytes Step Temp E_pair E_mol TotEng Press Volume 67 0 -1716.5189 0 -1716.5189 8858.2531 5046.0371 72 0 -1716.6031 0 -1716.6031 102.19249 5072.5665 Loop time of 0.451156 on 1 procs for 5 steps with 416 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 = -1716.51885241281 -1716.60302240477 -1716.60310310672 Force two-norm initial, final = 48.880071 0.84990048 Force max component initial, final = 32.384214 0.80743596 Final line search alpha, max atom move = 0.0010858467 0.00087675170 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.44894 | 0.44894 | 0.44894 | 0.0 | 99.51 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00048317 | 0.00048317 | 0.00048317 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001733 | | | 0.38 Nlocal: 416.000 ave 416 max 416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2568.00 ave 2568 max 2568 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: 22344.0 ave 22344 max 22344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 22344 Ave neighs/atom = 53.711538 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 = 7 28 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) = 4.953 | 4.953 | 4.953 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1716.6031 0 -1716.6031 102.19249 Loop time of 6.164e-06 on 1 procs for 0 steps with 416 atoms 178.5% 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 | | 6.164e-06 | | |100.00 Nlocal: 416.000 ave 416 max 416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2568.00 ave 2568 max 2568 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: 22328.0 ave 22328 max 22328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 22328 Ave neighs/atom = 53.673077 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 = 7 28 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) = 4.953 | 4.953 | 4.953 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 -1716.6031 -1716.6031 18.594238 74.526273 3.6604961 102.19249 102.19249 30.229253 20.39637 255.95185 2.3405866 126.66925 Loop time of 7.418e-06 on 1 procs for 0 steps with 416 atoms 283.1% 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 | | 7.418e-06 | | |100.00 Nlocal: 416.000 ave 416 max 416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2568.00 ave 2568 max 2568 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 11164.0 ave 11164 max 11164 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 22328.0 ave 22328 max 22328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 22328 Ave neighs/atom = 53.673077 Neighbor list builds = 0 Dangerous builds = 0 416 -1716.60310310672 eV 2.34058655601558 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08