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 = 3.5200001 3.5200001 3.5200001 Created orthogonal box = (0.0000000 -60.560371 0.0000000) to (30.280185 60.560371 3.5200001) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9103003 4.9103003 3.5200001 Created 592 atoms using lattice units in orthogonal box = (0.0000000 -60.560371 0.0000000) to (30.280185 60.560371 3.5200001) create_atoms CPU = 0.003 seconds 592 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9103003 4.9103003 3.5200001 Created 594 atoms using lattice units in orthogonal box = (0.0000000 -60.560371 0.0000000) to (30.280185 60.560371 3.5200001) create_atoms CPU = 0.002 seconds 594 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 = 6.85 ghost atom cutoff = 6.85 binsize = 3.425, bins = 9 36 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 6.85 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 1184 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_776437554506_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 = 6.85 ghost atom cutoff = 6.85 binsize = 3.425, bins = 9 36 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.85 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) = 5.051 | 5.051 | 5.051 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5104.3408 0 -5104.3408 19161.24 76 0 -5254.9519 0 -5254.9519 6216.5307 Loop time of 2.08901 on 1 procs for 76 steps with 1184 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 = -5104.34084485281 -5254.94700234082 -5254.95194082369 Force two-norm initial, final = 140.00750 0.25884884 Force max component initial, final = 34.402507 0.045890497 Final line search alpha, max atom move = 1.0000000 0.045890497 Iterations, force evaluations = 76 133 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.0025 | 2.0025 | 2.0025 | 0.0 | 95.86 Neigh | 0.040516 | 0.040516 | 0.040516 | 0.0 | 1.94 Comm | 0.025285 | 0.025285 | 0.025285 | 0.0 | 1.21 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02072 | | | 0.99 Nlocal: 1184.00 ave 1184 max 1184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8376.00 ave 8376 max 8376 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: 157648.0 ave 157648 max 157648 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 157648 Ave neighs/atom = 133.14865 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 = 6.85 ghost atom cutoff = 6.85 binsize = 3.425, bins = 9 36 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.85 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 76 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.051 | 5.051 | 5.051 Mbytes Step Temp E_pair E_mol TotEng Press Volume 76 0 -5254.9519 0 -5254.9519 6216.5307 12909.806 81 0 -5255.131 0 -5255.131 -18.189038 12954.783 Loop time of 0.126013 on 1 procs for 5 steps with 1184 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 = -5254.95194082369 -5255.13047330978 -5255.13096297378 Force two-norm initial, final = 104.05347 1.1594611 Force max component initial, final = 92.077252 1.0207967 Final line search alpha, max atom move = 0.00016255193 0.00016593247 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.12008 | 0.12008 | 0.12008 | 0.0 | 95.29 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0013695 | 0.0013695 | 0.0013695 | 0.0 | 1.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004563 | | | 3.62 Nlocal: 1184.00 ave 1184 max 1184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8376.00 ave 8376 max 8376 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: 157648.0 ave 157648 max 157648 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 157648 Ave neighs/atom = 133.14865 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 = 6.85 ghost atom cutoff = 6.85 binsize = 3.425, bins = 9 36 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.85 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) = 5.189 | 5.189 | 5.189 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5255.131 0 -5255.131 -18.189038 Loop time of 5.913e-06 on 1 procs for 0 steps with 1184 atoms 186.0% 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 | | 5.913e-06 | | |100.00 Nlocal: 1184.00 ave 1184 max 1184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8361.00 ave 8361 max 8361 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: 157624.0 ave 157624 max 157624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 157624 Ave neighs/atom = 133.12838 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 = 6.85 ghost atom cutoff = 6.85 binsize = 3.425, bins = 9 36 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.85 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) = 5.189 | 5.189 | 5.189 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 -5255.131 -5255.131 30.250407 121.55441 3.5231263 -18.189038 -18.189038 55.403795 16.387748 -126.35866 2.2370861 294.30812 Loop time of 6.505e-06 on 1 procs for 0 steps with 1184 atoms 261.3% 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 | | 6.505e-06 | | |100.00 Nlocal: 1184.00 ave 1184 max 1184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8361.00 ave 8361 max 8361 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 78812.0 ave 78812 max 78812 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 157624.0 ave 157624 max 157624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 157624 Ave neighs/atom = 133.12838 Neighbor list builds = 0 Dangerous builds = 0 1184 -5255.13096297378 eV 2.23708614195005 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02