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 = 3.5273294 3.5273294 3.5273294 Created orthogonal box = (0.0000000 -63.882652 0.0000000) to (22.585928 63.882652 4.9883971) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0596393 5.4533972 4.9883971 Created 656 atoms using lattice units in orthogonal box = (0.0000000 -63.882652 0.0000000) to (22.585928 63.882652 4.9883971) create_atoms CPU = 0.002 seconds 656 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0596393 5.4533972 4.9883971 Created 658 atoms using lattice units in orthogonal box = (0.0000000 -63.882652 0.0000000) to (22.585928 63.882652 4.9883971) create_atoms CPU = 0.002 seconds 658 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 = 10.13295 ghost atom cutoff = 10.13295 binsize = 5.066475, bins = 5 26 1 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 10.13295 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 1312 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_758825945924_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 = 10.13295 ghost atom cutoff = 10.13295 binsize = 5.066475, bins = 5 26 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.13295 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) = 6.773 | 6.773 | 6.773 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5311.5399 0 -5311.5399 29069.565 82 0 -5488.9306 0 -5488.9306 2983.1547 Loop time of 3.64282 on 1 procs for 82 steps with 1312 atoms 98.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5311.53987155344 -5488.92537526237 -5488.930594841 Force two-norm initial, final = 291.73361 0.32615380 Force max component initial, final = 95.965685 0.026440957 Final line search alpha, max atom move = 1.0000000 0.026440957 Iterations, force evaluations = 82 157 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.5682 | 3.5682 | 3.5682 | 0.0 | 97.95 Neigh | 0.029976 | 0.029976 | 0.029976 | 0.0 | 0.82 Comm | 0.028758 | 0.028758 | 0.028758 | 0.0 | 0.79 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01585 | | | 0.44 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13686.0 ave 13686 max 13686 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: 500436.0 ave 500436 max 500436 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 500436 Ave neighs/atom = 381.42988 Neighbor list builds = 1 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 = 10.13295 ghost atom cutoff = 10.13295 binsize = 5.066475, bins = 5 26 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.13295 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 82 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.768 | 6.768 | 6.768 Mbytes Step Temp E_pair E_mol TotEng Press Volume 82 0 -5488.9306 0 -5488.9306 2983.1547 14395.008 86 0 -5489.0693 0 -5489.0693 -92.880927 14418.63 Loop time of 0.154307 on 1 procs for 4 steps with 1312 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 = -5488.930594841 -5489.06881529934 -5489.06931426281 Force two-norm initial, final = 92.253744 2.1509270 Force max component initial, final = 78.013870 2.0536018 Final line search alpha, max atom move = 0.00016586854 0.00034062793 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.15009 | 0.15009 | 0.15009 | 0.0 | 97.27 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0007358 | 0.0007358 | 0.0007358 | 0.0 | 0.48 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00348 | | | 2.26 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13098.0 ave 13098 max 13098 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: 501060.0 ave 501060 max 501060 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 501060 Ave neighs/atom = 381.90549 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 = 10.13295 ghost atom cutoff = 10.13295 binsize = 5.066475, bins = 5 26 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.13295 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) = 6.906 | 6.906 | 6.906 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5489.0693 0 -5489.0693 -92.880927 Loop time of 2.47e-06 on 1 procs for 0 steps with 1312 atoms 161.9% 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 | | 2.47e-06 | | |100.00 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13102.0 ave 13102 max 13102 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: 500756.0 ave 500756 max 500756 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 500756 Ave neighs/atom = 381.67378 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 = 10.13295 ghost atom cutoff = 10.13295 binsize = 5.066475, bins = 5 26 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.13295 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) = 6.906 | 6.906 | 6.906 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 -5489.0693 -5489.0693 22.635317 127.9341 4.9791029 -92.880927 -92.880927 -228.69213 8.8218763 -58.772528 2.3514646 436.34606 Loop time of 3.035e-06 on 1 procs for 0 steps with 1312 atoms 230.6% 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 | | 3.035e-06 | | |100.00 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13102.0 ave 13102 max 13102 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 250378.0 ave 250378 max 250378 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 500756.0 ave 500756 max 500756 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 500756 Ave neighs/atom = 381.67378 Neighbor list builds = 0 Dangerous builds = 0 1312 -5489.06931426281 eV 2.35146458224461 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04