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 = 2.8700001 2.8700001 2.8700001 Created orthogonal box = (0.0000000 -46.983926 0.0000000) to (33.222653 46.983926 4.0587930) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9586049 4.5581421 4.0587930 Created 536 atoms using lattice units in orthogonal box = (0.0000000 -46.983926 0.0000000) to (33.222653 46.983926 4.0587930) create_atoms CPU = 0.002 seconds 536 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9586049 4.5581421 4.0587930 Created 538 atoms using lattice units in orthogonal box = (0.0000000 -46.983926 0.0000000) to (33.222653 46.983926 4.0587930) create_atoms CPU = 0.001 seconds 538 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 11 31 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 6.1615 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 1068 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_024705128470_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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 11 31 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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) = 4.603 | 4.603 | 4.603 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4299.1492 0 -4299.1492 28107.814 125 0 -4555.7677 0 -4555.7677 645.69854 Loop time of 0.894646 on 1 procs for 125 steps with 1068 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 = -4299.14915842577 -4555.76432886133 -4555.76768671009 Force two-norm initial, final = 265.17899 0.22064711 Force max component initial, final = 59.271303 0.041140374 Final line search alpha, max atom move = 1.0000000 0.041140374 Iterations, force evaluations = 125 228 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.85676 | 0.85676 | 0.85676 | 0.0 | 95.77 Neigh | 0.013386 | 0.013386 | 0.013386 | 0.0 | 1.50 Comm | 0.012459 | 0.012459 | 0.012459 | 0.0 | 1.39 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01204 | | | 1.35 Nlocal: 1068.00 ave 1068 max 1068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5583.00 ave 5583 max 5583 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: 70140.0 ave 70140 max 70140 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 70140 Ave neighs/atom = 65.674157 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 11 31 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 125 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.613 | 4.613 | 4.613 Mbytes Step Temp E_pair E_mol TotEng Press Volume 125 0 -4555.7677 0 -4555.7677 645.69854 12670.989 129 0 -4555.8778 0 -4555.8778 -63.821933 12676.587 Loop time of 0.0225823 on 1 procs for 4 steps with 1068 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 = -4555.76768671009 -4555.87714704025 -4555.87781423499 Force two-norm initial, final = 57.548065 0.91602265 Force max component initial, final = 51.196422 0.55601571 Final line search alpha, max atom move = 0.00028106525 0.00015627669 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.021051 | 0.021051 | 0.021051 | 0.0 | 93.22 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00028037 | 0.00028037 | 0.00028037 | 0.0 | 1.24 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001251 | | | 5.54 Nlocal: 1068.00 ave 1068 max 1068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6375.00 ave 6375 max 6375 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: 69700.0 ave 69700 max 69700 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 69700 Ave neighs/atom = 65.262172 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 11 31 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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) = 4.751 | 4.751 | 4.751 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4555.8778 0 -4555.8778 -63.821933 Loop time of 1.387e-06 on 1 procs for 0 steps with 1068 atoms 144.2% 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 | | 1.387e-06 | | |100.00 Nlocal: 1068.00 ave 1068 max 1068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6366.00 ave 6366 max 6366 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: 69576.0 ave 69576 max 69576 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 69576 Ave neighs/atom = 65.146067 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 11 31 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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) = 4.751 | 4.751 | 4.751 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 -4555.8778 -4555.8778 33.192678 94.272644 4.0511129 -63.821933 -63.821933 -70.210663 -53.692019 -67.563117 2.263797 495.57766 Loop time of 1.648e-06 on 1 procs for 0 steps with 1068 atoms 182.0% 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 | | 1.648e-06 | | |100.00 Nlocal: 1068.00 ave 1068 max 1068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6366.00 ave 6366 max 6366 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 34788.0 ave 34788 max 34788 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 69576.0 ave 69576 max 69576 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 69576 Ave neighs/atom = 65.146067 Neighbor list builds = 0 Dangerous builds = 0 1068 -4555.87770743499 eV 2.2637970152209 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01