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 = 4.0500000 4.0500000 4.0500000 Created orthogonal box = (0.0000000 -81.206297 0.0000000) to (46.882139 81.206297 7.0148058) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2976008 6.4638605 7.0148058 Created 1610 atoms using lattice units in orthogonal box = (0.0000000 -81.206297 0.0000000) to (46.882139 81.206297 7.0148058) create_atoms CPU = 0.010 seconds 1610 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2976008 6.4638605 7.0148058 Created 1610 atoms using lattice units in orthogonal box = (0.0000000 -81.206297 0.0000000) to (46.882139 81.206297 7.0148058) create_atoms CPU = 0.009 seconds 1610 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 ghost atom cutoff = 7 binsize = 3.5, bins = 14 47 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 32 atoms, new total = 3188 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_971738391444_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 ghost atom cutoff = 7 binsize = 3.5, bins = 14 47 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 5.784 | 5.784 | 5.784 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10625.143 0 -10625.143 -614.09512 35 0 -10658.959 0 -10658.959 -5403.3217 Loop time of 21.5639 on 1 procs for 35 steps with 3188 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 = -10625.1432595524 -10658.9505420115 -10658.9591755571 Force two-norm initial, final = 16.649441 0.27974105 Force max component initial, final = 2.5950196 0.023903297 Final line search alpha, max atom move = 0.79812960 0.019077928 Iterations, force evaluations = 35 60 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 21.487 | 21.487 | 21.487 | 0.0 | 99.64 Neigh | 0.043267 | 0.043267 | 0.043267 | 0.0 | 0.20 Comm | 0.013848 | 0.013848 | 0.013848 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02031 | | | 0.09 Nlocal: 3188.00 ave 3188 max 3188 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9103.00 ave 9103 max 9103 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: 249664.0 ave 249664 max 249664 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 249664 Ave neighs/atom = 78.313676 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 ghost atom cutoff = 7 binsize = 3.5, bins = 14 47 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 35 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.795 | 5.795 | 5.795 Mbytes Step Temp E_pair E_mol TotEng Press Volume 35 0 -10658.959 0 -10658.959 -5403.3217 53412.484 39 0 -10659.305 0 -10659.305 -1712.7932 53152.295 Loop time of 2.3933 on 1 procs for 4 steps with 3188 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 = -10658.959175557 -10659.3038686056 -10659.3049523877 Force two-norm initial, final = 197.80363 0.29624478 Force max component initial, final = 148.18192 0.031522823 Final line search alpha, max atom move = 0.00020116186 6.3411896e-06 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.3856 | 2.3856 | 2.3856 | 0.0 | 99.68 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0014295 | 0.0014295 | 0.0014295 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006298 | | | 0.26 Nlocal: 3188.00 ave 3188 max 3188 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9426.00 ave 9426 max 9426 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: 249880.0 ave 249880 max 249880 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 249880 Ave neighs/atom = 78.381430 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 ghost atom cutoff = 7 binsize = 3.5, bins = 14 47 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 5.949 | 5.949 | 5.949 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10659.305 0 -10659.305 -1712.7932 Loop time of 6.566e-06 on 1 procs for 0 steps with 3188 atoms 182.8% 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 | | 6.566e-06 | | |100.00 Nlocal: 3188.00 ave 3188 max 3188 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11029.0 ave 11029 max 11029 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: 256860.0 ave 256860 max 256860 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 256860 Ave neighs/atom = 80.570891 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 ghost atom cutoff = 7 binsize = 3.5, bins = 14 47 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 5.949 | 5.949 | 5.949 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 -10659.305 -10659.305 46.790981 162.41259 6.9942341 -1712.7932 -1712.7932 -0.94834895 -5136.9081 -0.52306373 2.3098026 1068.2531 Loop time of 6.786e-06 on 1 procs for 0 steps with 3188 atoms 280.0% 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 | | 6.786e-06 | | |100.00 Nlocal: 3188.00 ave 3188 max 3188 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11029.0 ave 11029 max 11029 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 128430.0 ave 128430 max 128430 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 256860.0 ave 256860 max 256860 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 256860 Ave neighs/atom = 80.570891 Neighbor list builds = 0 Dangerous builds = 0 3188 -10659.3049523877 eV 2.30980259796253 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:26