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 = 3.6111526 3.6111526 3.6111526 Created orthogonal box = (0.0000000 -72.403385 0.0000000) to (41.802114 72.403385 6.2546998) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6152093 5.7634535 6.2546998 Created 1608 atoms using lattice units in orthogonal box = (0.0000000 -72.403385 0.0000000) to (41.802114 72.403385 6.2546998) create_atoms CPU = 0.004 seconds 1608 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6152093 5.7634535 6.2546998 Created 1610 atoms using lattice units in orthogonal box = (0.0000000 -72.403385 0.0000000) to (41.802114 72.403385 6.2546998) create_atoms CPU = 0.004 seconds 1610 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 = 16 55 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, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 1 atoms, new total = 3217 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_137964310702_004#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 = 16 55 3 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) = 6.903 | 6.903 | 6.903 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13029.502 0 -13029.502 32849.181 67 0 -13626.203 0 -13626.203 5059.645 Loop time of 18.6823 on 1 procs for 67 steps with 3217 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 = -13029.5017408317 -13626.1911989817 -13626.203413302 Force two-norm initial, final = 658.80865 0.44349908 Force max component initial, final = 187.28033 0.12612402 Final line search alpha, max atom move = 0.57903099 0.073029714 Iterations, force evaluations = 67 110 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 18.554 | 18.554 | 18.554 | 0.0 | 99.32 Neigh | 0.099643 | 0.099643 | 0.099643 | 0.0 | 0.53 Comm | 0.010534 | 0.010534 | 0.010534 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01776 | | | 0.10 Nlocal: 3217.00 ave 3217 max 3217 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8351.00 ave 8351 max 8351 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: 173268.0 ave 173268 max 173268 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 173268 Ave neighs/atom = 53.860118 Neighbor list builds = 2 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 = 16 55 3 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) = 6.909 | 6.909 | 6.909 Mbytes Step Temp E_pair E_mol TotEng Press Volume 67 0 -13626.203 0 -13626.203 5059.645 37861.131 71 0 -13626.548 0 -13626.548 147.99254 37972.095 Loop time of 1.0298 on 1 procs for 4 steps with 3217 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 = -13626.203413302 -13626.5467639437 -13626.5479511947 Force two-norm initial, final = 239.82504 7.0993098 Force max component initial, final = 210.39821 6.1823310 Final line search alpha, max atom move = 0.00010033182 0.00062028451 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0265 | 1.0265 | 1.0265 | 0.0 | 99.68 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00041982 | 0.00041982 | 0.00041982 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002878 | | | 0.28 Nlocal: 3217.00 ave 3217 max 3217 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8344.00 ave 8344 max 8344 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: 173380.0 ave 173380 max 173380 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 173380 Ave neighs/atom = 53.894933 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 = 16 55 3 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) = 7.047 | 7.047 | 7.047 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13626.548 0 -13626.548 147.99254 Loop time of 2.537e-06 on 1 procs for 0 steps with 3217 atoms 197.1% 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 | | 2.537e-06 | | |100.00 Nlocal: 3217.00 ave 3217 max 3217 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8344.00 ave 8344 max 8344 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: 173350.0 ave 173350 max 173350 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 173350 Ave neighs/atom = 53.885608 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 = 16 55 3 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) = 7.047 | 7.047 | 7.047 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 -13626.548 -13626.548 41.822999 145.25148 6.2507023 147.99254 147.99254 43.586075 261.65543 138.73612 2.2411953 754.34359 Loop time of 2.396e-06 on 1 procs for 0 steps with 3217 atoms 250.4% 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 | | 2.396e-06 | | |100.00 Nlocal: 3217.00 ave 3217 max 3217 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8344.00 ave 8344 max 8344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 86675.0 ave 86675 max 86675 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 173350.0 ave 173350 max 173350 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 173350 Ave neighs/atom = 53.885608 Neighbor list builds = 0 Dangerous builds = 0 3217 -13626.5479511947 eV 2.24119527373105 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:20