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 = 3.0829274 3.0829274 3.0829274 Created orthogonal box = (0.0000000 -57.182868 0.0000000) to (20.216107 57.182868 4.3599177) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1715622 5.3190497 4.3599177 Created 346 atoms using lattice units in orthogonal box = (0.0000000 -57.182868 0.0000000) to (20.216107 57.182868 4.3599177) create_atoms CPU = 0.001 seconds 346 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1715622 5.3190497 4.3599177 Created 346 atoms using lattice units in orthogonal box = (0.0000000 -57.182868 0.0000000) to (20.216107 57.182868 4.3599177) create_atoms CPU = 0.001 seconds 346 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 7 35 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, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 4 atoms, new total = 688 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_152208847456_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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 7 35 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 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) = 5.294 | 5.294 | 5.294 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4288.835 0 -4288.835 62323.459 73 0 -4467.5373 0 -4467.5373 777.82586 Loop time of 24.8791 on 1 procs for 73 steps with 688 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 = -4288.83495379789 -4467.53314959109 -4467.5372948095 Force two-norm initial, final = 356.74232 0.28188285 Force max component initial, final = 90.383887 0.059696300 Final line search alpha, max atom move = 1.0000000 0.059696300 Iterations, force evaluations = 73 139 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 24.846 | 24.846 | 24.846 | 0.0 | 99.87 Neigh | 0.022846 | 0.022846 | 0.022846 | 0.0 | 0.09 Comm | 0.0054256 | 0.0054256 | 0.0054256 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004668 | | | 0.02 Nlocal: 688.000 ave 688 max 688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4424.00 ave 4424 max 4424 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: 49976.0 ave 49976 max 49976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 49976 Ave neighs/atom = 72.639535 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 7 35 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 73 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.294 | 5.294 | 5.294 Mbytes Step Temp E_pair E_mol TotEng Press Volume 73 0 -4467.5373 0 -4467.5373 777.82586 10080.26 75 0 -4467.5591 0 -4467.5591 4150.7404 10064.692 Loop time of 0.900244 on 1 procs for 2 steps with 688 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 = -4467.5372948095 -4467.55857130567 -4467.55911945497 Force two-norm initial, final = 37.691540 0.29143971 Force max component initial, final = 30.958482 0.061273878 Final line search alpha, max atom move = 0.00030905530 1.8937017e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.89941 | 0.89941 | 0.89941 | 0.0 | 99.91 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00017104 | 0.00017104 | 0.00017104 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0006638 | | | 0.07 Nlocal: 688.000 ave 688 max 688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4424.00 ave 4424 max 4424 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: 49936.0 ave 49936 max 49936 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 49936 Ave neighs/atom = 72.581395 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 7 35 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 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) = 5.814 | 5.814 | 5.814 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4467.5591 0 -4467.5591 4150.7404 Loop time of 1.669e-06 on 1 procs for 0 steps with 688 atoms 179.7% 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 | | 1.669e-06 | | |100.00 Nlocal: 688.000 ave 688 max 688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4424.00 ave 4424 max 4424 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: 50240.0 ave 50240 max 50240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 50240 Ave neighs/atom = 73.023256 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 7 35 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 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) = 5.814 | 5.814 | 5.814 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 -4467.5591 -4467.5591 20.207028 114.36574 4.3551402 4150.7404 4150.7404 -5.1798503 12454.586 2.8150257 2.5330109 1496.5995 Loop time of 1.546e-06 on 1 procs for 0 steps with 688 atoms 194.0% 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 | | 1.546e-06 | | |100.00 Nlocal: 688.000 ave 688 max 688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4424.00 ave 4424 max 4424 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 25120.0 ave 25120 max 25120 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 50240.0 ave 50240 max 50240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 50240 Ave neighs/atom = 73.023256 Neighbor list builds = 0 Dangerous builds = 0 688 -4467.55911945497 eV 2.53301085039366 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:26