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 -42.538195 0.0000000) to (21.267274 42.538195 3.6473074) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0040645 5.0040645 3.6473074 Created 274 atoms using lattice units in orthogonal box = (0.0000000 -42.538195 0.0000000) to (21.267274 42.538195 3.6473074) create_atoms CPU = 0.002 seconds 274 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0040645 5.0040645 3.6473074 Created 274 atoms using lattice units in orthogonal box = (0.0000000 -42.538195 0.0000000) to (21.267274 42.538195 3.6473074) 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 8 atoms, new total = 540 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 = 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) = 4.846 | 4.846 | 4.846 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2208.0502 0 -2208.0502 8141.715 39 0 -2229.3165 0 -2229.3165 -4246.2515 Loop time of 5.24114 on 1 procs for 39 steps with 540 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 = -2208.05017137974 -2229.31462110477 -2229.31650946539 Force two-norm initial, final = 32.458990 0.39185117 Force max component initial, final = 10.256316 0.16624911 Final line search alpha, max atom move = 1.0000000 0.16624911 Iterations, force evaluations = 39 70 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.2317 | 5.2317 | 5.2317 | 0.0 | 99.82 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0043026 | 0.0043026 | 0.0043026 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005173 | | | 0.10 Nlocal: 540.000 ave 540 max 540 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2682.00 ave 2682 max 2682 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: 28884.0 ave 28884 max 28884 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 28884 Ave neighs/atom = 53.488889 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 : 39 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 39 0 -2229.3165 0 -2229.3165 -4246.2515 6599.2298 43 0 -2229.3435 0 -2229.3435 -1203.2866 6586.8107 Loop time of 0.496254 on 1 procs for 4 steps with 540 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 = -2229.31650946539 -2229.34348245522 -2229.34352425955 Force two-norm initial, final = 24.664709 0.75160272 Force max component initial, final = 23.231610 0.49426857 Final line search alpha, max atom move = 0.0018850606 0.00093172619 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.49405 | 0.49405 | 0.49405 | 0.0 | 99.56 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00040896 | 0.00040896 | 0.00040896 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001795 | | | 0.36 Nlocal: 540.000 ave 540 max 540 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2664.00 ave 2664 max 2664 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: 28880.0 ave 28880 max 28880 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 28880 Ave neighs/atom = 53.481481 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 -2229.3435 0 -2229.3435 -1203.2866 Loop time of 6.616e-06 on 1 procs for 0 steps with 540 atoms 166.3% 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 | | 6.616e-06 | | |100.00 Nlocal: 540.000 ave 540 max 540 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2670.00 ave 2670 max 2670 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: 28896.0 ave 28896 max 28896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 28896 Ave neighs/atom = 53.511111 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 -2229.3435 -2229.3435 21.212166 85.076391 3.6499012 -1203.2866 -1203.2866 97.417797 -3827.5891 120.31143 2.3104284 95.479997 Loop time of 6.596e-06 on 1 procs for 0 steps with 540 atoms 242.6% 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 | | 6.596e-06 | | |100.00 Nlocal: 540.000 ave 540 max 540 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2670.00 ave 2670 max 2670 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 14448.0 ave 14448 max 14448 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 28896.0 ave 28896 max 28896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 28896 Ave neighs/atom = 53.511111 Neighbor list builds = 0 Dangerous builds = 0 540 -2229.34352425955 eV 2.31042838308014 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06