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 = 4.0469996 4.0469996 4.0469996 Created orthogonal box = (0.0000000 -77.423660 0.0000000) to (44.700571 77.423660 7.0096089) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.5951662 5.9231216 7.0096089 Created 1463 atoms using lattice units in orthogonal box = (0.0000000 -77.423660 0.0000000) to (44.700571 77.423660 7.0096089) create_atoms CPU = 0.003 seconds 1463 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.5951662 5.9231216 7.0096089 Created 1465 atoms using lattice units in orthogonal box = (0.0000000 -77.423660 0.0000000) to (44.700571 77.423660 7.0096089) create_atoms CPU = 0.003 seconds 1465 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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 13 44 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 7.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 5 atoms, new total = 2923 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_958395190627_001#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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 13 44 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.1 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) = 5.803 | 5.803 | 5.803 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9557.5315 0 -9557.5315 13473.057 77 0 -9797.6368 0 -9797.6368 1884.5187 Loop time of 19.3015 on 1 procs for 77 steps with 2923 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 = -9557.53152411808 -9797.62760717524 -9797.63684532523 Force two-norm initial, final = 300.94821 0.35320068 Force max component initial, final = 60.501530 0.094899240 Final line search alpha, max atom move = 0.85893743 0.081512509 Iterations, force evaluations = 77 143 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 19.213 | 19.213 | 19.213 | 0.0 | 99.54 Neigh | 0.041638 | 0.041638 | 0.041638 | 0.0 | 0.22 Comm | 0.023626 | 0.023626 | 0.023626 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02281 | | | 0.12 Nlocal: 2923.00 ave 2923 max 2923 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10926.0 ave 10926 max 10926 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: 250658.0 ave 250658 max 250658 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 250658 Ave neighs/atom = 85.753678 Neighbor list builds = 2 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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 13 44 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 77 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.799 | 5.799 | 5.799 Mbytes Step Temp E_pair E_mol TotEng Press Volume 77 0 -9797.6368 0 -9797.6368 1884.5187 48518.856 81 0 -9797.8015 0 -9797.8015 -72.713402 48639.384 Loop time of 0.824904 on 1 procs for 4 steps with 2923 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 = -9797.63684532521 -9797.79827059853 -9797.80152433211 Force two-norm initial, final = 114.79542 5.7726318 Force max component initial, final = 104.62525 4.2038435 Final line search alpha, max atom move = 5.1747181e-05 0.00021753705 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.82127 | 0.82127 | 0.82127 | 0.0 | 99.56 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0005307 | 0.0005307 | 0.0005307 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003102 | | | 0.38 Nlocal: 2923.00 ave 2923 max 2923 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10460.0 ave 10460 max 10460 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: 250684.0 ave 250684 max 250684 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 250684 Ave neighs/atom = 85.762573 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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 13 44 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.1 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) = 5.937 | 5.937 | 5.937 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9797.8015 0 -9797.8015 -72.713402 Loop time of 2.299e-06 on 1 procs for 0 steps with 2923 atoms 174.0% 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 | | 2.299e-06 | | |100.00 Nlocal: 2923.00 ave 2923 max 2923 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10466.0 ave 10466 max 10466 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: 250540.0 ave 250540 max 250540 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 250540 Ave neighs/atom = 85.713308 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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 13 44 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.1 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) = 5.937 | 5.937 | 5.937 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 -9797.8015 -9797.8015 44.675992 155.3677 7.0073388 -72.713402 -72.713402 -122.28429 42.573431 -138.42934 2.4810723 1677.5782 Loop time of 2.751e-06 on 1 procs for 0 steps with 2923 atoms 290.8% 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 | | 2.751e-06 | | |100.00 Nlocal: 2923.00 ave 2923 max 2923 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10466.0 ave 10466 max 10466 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 125270.0 ave 125270 max 125270 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 250540.0 ave 250540 max 250540 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 250540 Ave neighs/atom = 85.713308 Neighbor list builds = 0 Dangerous builds = 0 2923 -9797.80152433211 eV 2.48107229170535 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:21