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 = 2.8552583 2.8552583 2.8552583 Created orthogonal box = (0.0000000 -50.433917 0.0000000) to (29.118036 50.433917 4.9454524) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.4796978 4.5261207 4.9454524 Created 623 atoms using lattice units in orthogonal box = (0.0000000 -50.433917 0.0000000) to (29.118036 50.433917 4.9454524) create_atoms CPU = 0.001 seconds 623 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.4796978 4.5261207 4.9454524 Created 627 atoms using lattice units in orthogonal box = (0.0000000 -50.433917 0.0000000) to (29.118036 50.433917 4.9454524) create_atoms CPU = 0.001 seconds 627 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 8 26 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 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 1248 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_942420706858_005#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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 8 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 5.462 | 5.462 | 5.462 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4356.6239 0 -4356.6239 133950 72 0 -5137.5531 0 -5137.5531 2537.8857 Loop time of 1.31117 on 1 procs for 72 steps with 1248 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4356.62387412988 -5137.54827086955 -5137.55314413828 Force two-norm initial, final = 878.76416 0.23548417 Force max component initial, final = 138.34246 0.040453698 Final line search alpha, max atom move = 1.0000000 0.040453698 Iterations, force evaluations = 72 127 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.282 | 1.282 | 1.282 | 0.0 | 97.78 Neigh | 0.012421 | 0.012421 | 0.012421 | 0.0 | 0.95 Comm | 0.0091102 | 0.0091102 | 0.0091102 | 0.0 | 0.69 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007612 | | | 0.58 Nlocal: 1248.00 ave 1248 max 1248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8004.00 ave 8004 max 8004 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: 211208.0 ave 211208 max 211208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 211208 Ave neighs/atom = 169.23718 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 8 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 72 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.463 | 5.463 | 5.463 Mbytes Step Temp E_pair E_mol TotEng Press Volume 72 0 -5137.5531 0 -5137.5531 2537.8857 14525.156 75 0 -5137.6023 0 -5137.6023 -2.2874474 14546.359 Loop time of 0.0615553 on 1 procs for 3 steps with 1248 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 = -5137.5531441383 -5137.6020629721 -5137.60229895975 Force two-norm initial, final = 51.622662 0.36014095 Force max component initial, final = 44.772445 0.23305954 Final line search alpha, max atom move = 0.00026078072 6.0777434e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.059637 | 0.059637 | 0.059637 | 0.0 | 96.88 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00038957 | 0.00038957 | 0.00038957 | 0.0 | 0.63 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001528 | | | 2.48 Nlocal: 1248.00 ave 1248 max 1248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8130.00 ave 8130 max 8130 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: 211180.0 ave 211180 max 211180 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 211180 Ave neighs/atom = 169.21474 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 8 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 5.601 | 5.601 | 5.601 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5137.6023 0 -5137.6023 -2.2874474 Loop time of 1.754e-06 on 1 procs for 0 steps with 1248 atoms 171.0% 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 | | 1.754e-06 | | |100.00 Nlocal: 1248.00 ave 1248 max 1248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8130.00 ave 8130 max 8130 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: 211148.0 ave 211148 max 211148 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 211148 Ave neighs/atom = 169.18910 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 8 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 5.601 | 5.601 | 5.601 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 -5137.6023 -5137.6023 29.089943 101.05126 4.9484558 -2.2874474 -2.2874474 8.540215 10.282858 -25.685415 2.2494846 540.09621 Loop time of 2.033e-06 on 1 procs for 0 steps with 1248 atoms 196.8% 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 | | 2.033e-06 | | |100.00 Nlocal: 1248.00 ave 1248 max 1248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8130.00 ave 8130 max 8130 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 105574.0 ave 105574 max 105574 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 211148.0 ave 211148 max 211148 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 211148 Ave neighs/atom = 169.18910 Neighbor list builds = 0 Dangerous builds = 0 1248 -5137.60229895975 eV 2.24948457818671 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01