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 = 3.5213917 3.5213917 3.5213917 Created orthogonal box = (0.0000000 -57.651189 0.0000000) to (40.763057 57.651189 4.9800000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0840383 5.5926842 4.9800000 Created 1080 atoms using lattice units in orthogonal box = (0.0000000 -57.651189 0.0000000) to (40.763057 57.651189 4.9800000) create_atoms CPU = 0.002 seconds 1080 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0840383 5.5926842 4.9800000 Created 1080 atoms using lattice units in orthogonal box = (0.0000000 -57.651189 0.0000000) to (40.763057 57.651189 4.9800000) create_atoms CPU = 0.002 seconds 1080 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 14 37 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, cut 6.25 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 2144 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_461927113651_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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 14 37 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 5.234 | 5.234 | 5.234 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9419.6519 0 -9419.6519 18964.533 42 0 -9518.2126 0 -9518.2126 4458.8504 Loop time of 5.57253 on 1 procs for 42 steps with 2144 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -9419.65187742047 -9518.20385859428 -9518.21256121943 Force two-norm initial, final = 93.714097 0.31638831 Force max component initial, final = 13.599274 0.024899817 Final line search alpha, max atom move = 1.0000000 0.024899817 Iterations, force evaluations = 42 76 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.5537 | 5.5537 | 5.5537 | 0.0 | 99.66 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0092079 | 0.0092079 | 0.0092079 | 0.0 | 0.17 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009666 | | | 0.17 Nlocal: 2144.00 ave 2144 max 2144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8741.00 ave 8741 max 8741 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: 185168.0 ave 185168 max 185168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 185168 Ave neighs/atom = 86.365672 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 14 37 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 42 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.234 | 5.234 | 5.234 Mbytes Step Temp E_pair E_mol TotEng Press Volume 42 0 -9518.2126 0 -9518.2126 4458.8504 23406.385 44 0 -9518.2688 0 -9518.2688 1320.6767 23445.622 Loop time of 0.286977 on 1 procs for 2 steps with 2144 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 = -9518.21256121943 -9518.26469554451 -9518.26880584589 Force two-norm initial, final = 81.624724 5.6006463 Force max component initial, final = 77.000419 5.4657550 Final line search alpha, max atom move = 5.1992803e-05 0.00028417992 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.28532 | 0.28532 | 0.28532 | 0.0 | 99.42 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00028358 | 0.00028358 | 0.00028358 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001372 | | | 0.48 Nlocal: 2144.00 ave 2144 max 2144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8720.00 ave 8720 max 8720 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: 184992.0 ave 184992 max 184992 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 184992 Ave neighs/atom = 86.283582 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 14 37 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 pair build: full/bin/atomonly stencil: full/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) = 5.372 | 5.372 | 5.372 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9518.2688 0 -9518.2688 1320.6767 Loop time of 1.98e-06 on 1 procs for 0 steps with 2144 atoms 202.0% 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 | | 1.98e-06 | | |100.00 Nlocal: 2144.00 ave 2144 max 2144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8720.00 ave 8720 max 8720 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: 184960.0 ave 184960 max 184960 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 184960 Ave neighs/atom = 86.268657 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 14 37 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 pair build: full/bin/atomonly stencil: full/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) = 5.372 | 5.372 | 5.372 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 -9518.2688 -9518.2688 40.820538 115.30238 4.9813239 1320.6767 1320.6767 -80.747649 4416.3839 -373.6063 2.3274183 839.29982 Loop time of 2.816e-06 on 1 procs for 0 steps with 2144 atoms 284.1% 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 | | 2.816e-06 | | |100.00 Nlocal: 2144.00 ave 2144 max 2144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8720.00 ave 8720 max 8720 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 92480.0 ave 92480 max 92480 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 184960.0 ave 184960 max 184960 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 184960 Ave neighs/atom = 86.268657 Neighbor list builds = 0 Dangerous builds = 0 2144 -9518.26880584589 eV 2.32741827482234 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06