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 = 3.1465590 3.1465590 3.1465590 Created orthogonal box = (0.0000000 -36.427200 0.0000000) to (25.755695 36.427200 4.4499063) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9973737 5.4364259 4.4499063 Created 269 atoms using lattice units in orthogonal box = (0.0000000 -36.427200 0.0000000) to (25.755695 36.427200 4.4499063) create_atoms CPU = 0.003 seconds 269 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9973737 5.4364259 4.4499063 Created 269 atoms using lattice units in orthogonal box = (0.0000000 -36.427200 0.0000000) to (25.755695 36.427200 4.4499063) create_atoms CPU = 0.002 seconds 269 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 9 26 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 5.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 3 atoms, new total = 535 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_805823015127_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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 9 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.459 | 4.459 | 4.459 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3595.4317 0 -3595.4317 19896.448 32 0 -3619.3296 0 -3619.3296 8658.7537 Loop time of 1.77959 on 1 procs for 32 steps with 535 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 = -3595.43170912661 -3619.32627756262 -3619.329636912 Force two-norm initial, final = 24.706857 0.17973157 Force max component initial, final = 5.2157026 0.019784149 Final line search alpha, max atom move = 1.0000000 0.019784149 Iterations, force evaluations = 32 57 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.7707 | 1.7707 | 1.7707 | 0.0 | 99.50 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0039151 | 0.0039151 | 0.0039151 | 0.0 | 0.22 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005024 | | | 0.28 Nlocal: 535.000 ave 535 max 535 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2629.00 ave 2629 max 2629 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: 30732.0 ave 30732 max 30732 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30732 Ave neighs/atom = 57.442991 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 9 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 32 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.459 | 4.459 | 4.459 Mbytes Step Temp E_pair E_mol TotEng Press Volume 32 0 -3619.3296 0 -3619.3296 8658.7537 8349.8741 35 0 -3619.3886 0 -3619.3886 2157.6447 8370.4203 Loop time of 0.182727 on 1 procs for 3 steps with 535 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 = -3619.329636912 -3619.38653415049 -3619.38861790682 Force two-norm initial, final = 56.759918 0.19087708 Force max component initial, final = 50.542920 0.018975906 Final line search alpha, max atom move = 0.00013836594 2.6256191e-06 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.18094 | 0.18094 | 0.18094 | 0.0 | 99.02 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00034824 | 0.00034824 | 0.00034824 | 0.0 | 0.19 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001438 | | | 0.79 Nlocal: 535.000 ave 535 max 535 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2606.00 ave 2606 max 2606 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: 30714.0 ave 30714 max 30714 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30714 Ave neighs/atom = 57.409346 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 9 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.597 | 4.597 | 4.597 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3619.3886 0 -3619.3886 2157.6447 Loop time of 3.3878e-05 on 1 procs for 0 steps with 535 atoms 32.5% 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 | | 3.388e-05 | | |100.00 Nlocal: 535.000 ave 535 max 535 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2606.00 ave 2606 max 2606 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: 30714.0 ave 30714 max 30714 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30714 Ave neighs/atom = 57.409346 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 9 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.597 | 4.597 | 4.597 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 -3619.3886 -3619.3886 25.762065 72.8544 4.4597531 2157.6447 2157.6447 -0.22546363 6472.3508 0.80864714 2.3347642 474.51363 Loop time of 6.375e-06 on 1 procs for 0 steps with 535 atoms 251.0% 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 | | 6.375e-06 | | |100.00 Nlocal: 535.000 ave 535 max 535 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2606.00 ave 2606 max 2606 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 15357.0 ave 15357 max 15357 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 30714.0 ave 30714 max 30714 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30714 Ave neighs/atom = 57.409346 Neighbor list builds = 0 Dangerous builds = 0 535 -3619.38861790682 eV 2.33476420093234 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02