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 = 4.0415970 4.0415970 4.0415970 Created orthogonal box = (0.0000000 -55.562773 0.0000000) to (15.122271 55.562773 9.8998505) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.4809734 6.1736414 6.5999003 Created 504 atoms using lattice units in orthogonal box = (0.0000000 -55.562773 0.0000000) to (15.122271 55.562773 9.8998505) create_atoms CPU = 0.001 seconds 504 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.4809734 6.1736414 6.5999003 Created 508 atoms using lattice units in orthogonal box = (0.0000000 -55.562773 0.0000000) to (15.122271 55.562773 9.8998505) create_atoms CPU = 0.001 seconds 508 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 = 6.04112 ghost atom cutoff = 6.04112 binsize = 3.02056, bins = 6 37 4 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, ghost, cut 6.04112 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 4 atoms, new total = 1008 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_736419017411_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 = 6.04112 ghost atom cutoff = 6.04112 binsize = 3.02056, bins = 6 37 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.04112 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 4.898 | 4.898 | 4.898 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3346.3285 0 -3346.3285 10412.601 39 0 -3384.4982 0 -3384.4982 14025.987 Loop time of 12.2327 on 1 procs for 39 steps with 1008 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 = -3346.32851045501 -3384.49508699744 -3384.49821861107 Force two-norm initial, final = 44.866842 0.15994689 Force max component initial, final = 8.8543055 0.011063584 Final line search alpha, max atom move = 1.0000000 0.011063584 Iterations, force evaluations = 39 72 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 12.222 | 12.222 | 12.222 | 0.0 | 99.91 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0042856 | 0.0042856 | 0.0042856 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006404 | | | 0.05 Nlocal: 1008.00 ave 1008 max 1008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3472.00 ave 3472 max 3472 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: 54552.0 ave 54552 max 54552 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 54552 Ave neighs/atom = 54.119048 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 = 6.04112 ghost atom cutoff = 6.04112 binsize = 3.02056, bins = 6 37 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.04112 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 39 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.280 | 5.280 | 5.280 Mbytes Step Temp E_pair E_mol TotEng Press Volume 39 0 -3384.4982 0 -3384.4982 14025.987 16636.408 49 0 -3385.4013 0 -3385.4013 419.28778 16790.769 Loop time of 2.25055 on 1 procs for 10 steps with 1008 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 = -3384.49821861106 -3385.39868905081 -3385.40131412157 Force two-norm initial, final = 270.35078 7.6540379 Force max component initial, final = 223.57360 4.9551831 Final line search alpha, max atom move = 0.00016178603 0.00080167941 Iterations, force evaluations = 10 11 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.207 | 2.207 | 2.207 | 0.0 | 98.07 Neigh | 0.037832 | 0.037832 | 0.037832 | 0.0 | 1.68 Comm | 0.00094132 | 0.00094132 | 0.00094132 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004774 | | | 0.21 Nlocal: 1008.00 ave 1008 max 1008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3543.00 ave 3543 max 3543 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: 54128.0 ave 54128 max 54128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 54128 Ave neighs/atom = 53.698413 Neighbor list builds = 1 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 = 6.04112 ghost atom cutoff = 6.04112 binsize = 3.02056, bins = 6 38 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.04112 pair build: full/bin/ghost stencil: full/ghost/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) = 5.418 | 5.418 | 5.418 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3385.4013 0 -3385.4013 419.28778 Loop time of 3.566e-06 on 1 procs for 0 steps with 1008 atoms 140.2% 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 | | 3.566e-06 | | |100.00 Nlocal: 1008.00 ave 1008 max 1008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3543.00 ave 3543 max 3543 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: 54128.0 ave 54128 max 54128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 54128 Ave neighs/atom = 53.698413 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 = 6.04112 ghost atom cutoff = 6.04112 binsize = 3.02056, bins = 6 38 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.04112 pair build: full/bin/ghost stencil: full/ghost/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) = 5.418 | 5.418 | 5.418 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 -3385.4013 -3385.4013 15.129967 112.17801 9.8929292 419.28778 419.28778 351.07694 477.30204 429.48435 2.5473698 543.32932 Loop time of 3.503e-06 on 1 procs for 0 steps with 1008 atoms 142.7% 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 | | 3.503e-06 | | |100.00 Nlocal: 1008.00 ave 1008 max 1008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3543.00 ave 3543 max 3543 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 27064.0 ave 27064 max 27064 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 54128.0 ave 54128 max 54128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 54128 Ave neighs/atom = 53.698413 Neighbor list builds = 0 Dangerous builds = 0 1008 -3385.40131412157 eV 2.54736982827338 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:15