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 = 3.5200008 3.5200008 3.5200008 Created orthogonal box = (0.0000000 -42.535851 0.0000000) to (52.091254 42.535851 8.6222058) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9950518 5.2437121 5.7481372 Created 1756 atoms using lattice units in orthogonal box = (0.0000000 -42.535851 0.0000000) to (52.091254 42.535851 8.6222058) create_atoms CPU = 0.007 seconds 1756 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9950518 5.2437121 5.7481372 Created 1756 atoms using lattice units in orthogonal box = (0.0000000 -42.535851 0.0000000) to (52.091254 42.535851 8.6222058) create_atoms CPU = 0.006 seconds 1756 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 14 22 3 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 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 56 atoms, new total = 3456 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_820335782779_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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 14 22 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 7.388 | 7.388 | 7.388 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15239.138 0 -15239.138 -4108.0215 71 0 -15313.195 0 -15313.195 -18560.505 Loop time of 8.10856 on 1 procs for 71 steps with 3456 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 = -15239.1380370081 -15313.1804451348 -15313.1945913933 Force two-norm initial, final = 33.331188 0.49968915 Force max component initial, final = 4.3845660 0.059642124 Final line search alpha, max atom move = 1.0000000 0.059642124 Iterations, force evaluations = 71 129 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.9477 | 7.9477 | 7.9477 | 0.0 | 98.02 Neigh | 0.084605 | 0.084605 | 0.084605 | 0.0 | 1.04 Comm | 0.032979 | 0.032979 | 0.032979 | 0.0 | 0.41 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04331 | | | 0.53 Nlocal: 3456.00 ave 3456 max 3456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11145.0 ave 11145 max 11145 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: 609904.0 ave 609904 max 609904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 609904 Ave neighs/atom = 176.47685 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 14 22 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 71 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.389 | 7.389 | 7.389 Mbytes Step Temp E_pair E_mol TotEng Press Volume 71 0 -15313.195 0 -15313.195 -18560.505 38209.233 76 0 -15314.681 0 -15314.681 -4380.748 37917.682 Loop time of 0.434883 on 1 procs for 5 steps with 3456 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 = -15313.1945913932 -15314.6710817893 -15314.6812955117 Force two-norm initial, final = 546.81344 11.385983 Force max component initial, final = 417.46512 11.030823 Final line search alpha, max atom move = 2.4317447e-05 0.00026824146 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.4258 | 0.4258 | 0.4258 | 0.0 | 97.91 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.001688 | 0.001688 | 0.001688 | 0.0 | 0.39 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007393 | | | 1.70 Nlocal: 3456.00 ave 3456 max 3456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11162.0 ave 11162 max 11162 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: 609752.0 ave 609752 max 609752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 609752 Ave neighs/atom = 176.43287 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 14 22 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 7.527 | 7.527 | 7.527 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15314.681 0 -15314.681 -4380.748 Loop time of 6.395e-06 on 1 procs for 0 steps with 3456 atoms 172.0% 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 | | 6.395e-06 | | |100.00 Nlocal: 3456.00 ave 3456 max 3456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11214.0 ave 11214 max 11214 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: 612042.0 ave 612042 max 612042 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 612042 Ave neighs/atom = 177.09549 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 14 22 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 7.527 | 7.527 | 7.527 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 -15314.681 -15314.681 51.858451 85.071702 8.5948266 -4380.748 -4380.748 -112.41398 -13494.447 464.61716 2.2495925 1460.044 Loop time of 6.976e-06 on 1 procs for 0 steps with 3456 atoms 315.4% 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 | | 6.976e-06 | | |100.00 Nlocal: 3456.00 ave 3456 max 3456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11214.0 ave 11214 max 11214 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 306021.0 ave 306021 max 306021 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 612042.0 ave 612042 max 612042 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 612042 Ave neighs/atom = 177.09549 Neighbor list builds = 0 Dangerous builds = 0 3456 -15314.6812955117 eV 2.24959248259354 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:09