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 -42.112915 0.0000000) to (21.056457 42.112915 3.6111526) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9544605 4.9544605 3.6111526 Created 272 atoms using lattice units in orthogonal box = (0.0000000 -42.112915 0.0000000) to (21.056457 42.112915 3.6111526) create_atoms CPU = 0.002 seconds 272 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9544605 4.9544605 3.6111526 Created 274 atoms using lattice units in orthogonal box = (0.0000000 -42.112915 0.0000000) to (21.056457 42.112915 3.6111526) create_atoms CPU = 0.001 seconds 274 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 = 8 32 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 0 atoms, new total = 546 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 = 8 32 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) = 4.849 | 4.849 | 4.849 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2123.1824 0 -2123.1824 65230.227 125 0 -2308.5793 0 -2308.5793 12662.077 Loop time of 17.1633 on 1 procs for 125 steps with 546 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 = -2123.18238007434 -2308.57733383049 -2308.57932867472 Force two-norm initial, final = 346.60359 0.25930400 Force max component initial, final = 141.34349 0.10159627 Final line search alpha, max atom move = 1.0000000 0.10159627 Iterations, force evaluations = 125 236 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 17.127 | 17.127 | 17.127 | 0.0 | 99.79 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.017955 | 0.017955 | 0.017955 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01791 | | | 0.10 Nlocal: 546.000 ave 546 max 546 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3186.00 ave 3186 max 3186 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: 29608.0 ave 29608 max 29608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29608 Ave neighs/atom = 54.227106 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 = 8 32 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 : 125 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.846 | 4.846 | 4.846 Mbytes Step Temp E_pair E_mol TotEng Press Volume 125 0 -2308.5793 0 -2308.5793 12662.077 6404.3704 133 0 -2308.861 0 -2308.861 -197.67334 6452.5771 Loop time of 0.706898 on 1 procs for 8 steps with 546 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2308.57932867472 -2308.86052435057 -2308.86104850521 Force two-norm initial, final = 92.814602 2.0878114 Force max component initial, final = 64.525493 1.4746498 Final line search alpha, max atom move = 0.00026681188 0.00039345407 Iterations, force evaluations = 8 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.70388 | 0.70388 | 0.70388 | 0.0 | 99.57 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00059959 | 0.00059959 | 0.00059959 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002416 | | | 0.34 Nlocal: 546.000 ave 546 max 546 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2694.00 ave 2694 max 2694 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: 29428.0 ave 29428 max 29428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29428 Ave neighs/atom = 53.897436 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 = 8 32 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) = 4.984 | 4.984 | 4.984 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2308.861 0 -2308.861 -197.67334 Loop time of 6.354e-06 on 1 procs for 0 steps with 546 atoms 0.0% 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 | | 6.354e-06 | | |100.00 Nlocal: 546.000 ave 546 max 546 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2697.00 ave 2697 max 2697 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: 29424.0 ave 29424 max 29424 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29424 Ave neighs/atom = 53.890110 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 = 8 32 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) = 4.984 | 4.984 | 4.984 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 -2308.861 -2308.861 21.01021 84.445891 3.6368408 -197.67334 -197.67334 -330.12358 -367.11258 104.21613 2.2704085 146.8861 Loop time of 6.796e-06 on 1 procs for 0 steps with 546 atoms 250.1% 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 | | 6.796e-06 | | |100.00 Nlocal: 546.000 ave 546 max 546 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2697.00 ave 2697 max 2697 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 14712.0 ave 14712 max 14712 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 29424.0 ave 29424 max 29424 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29424 Ave neighs/atom = 53.890110 Neighbor list builds = 0 Dangerous builds = 0 546 -2308.86104850521 eV 2.27040848590549 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:18