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 = 3.5200000 3.5200000 3.5200000 Created orthogonal box = (0.0000000 -43.397475 0.0000000) to (15.343324 43.397475 4.9780317) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6528037 4.5681552 4.9780317 Created 304 atoms using lattice units in orthogonal box = (0.0000000 -43.397475 0.0000000) to (15.343324 43.397475 4.9780317) create_atoms CPU = 0.002 seconds 304 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6528037 4.5681552 4.9780317 Created 306 atoms using lattice units in orthogonal box = (0.0000000 -43.397475 0.0000000) to (15.343324 43.397475 4.9780317) create_atoms CPU = 0.002 seconds 306 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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 4 21 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 8.4527 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 606 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_592013496703_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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 4 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4527 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) = 4.957 | 4.957 | 4.957 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2415.7383 0 -2415.7383 54880.749 78 0 -2686.7397 0 -2686.7397 2450.2429 Loop time of 2.19719 on 1 procs for 78 steps with 606 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2415.73826246645 -2686.73720382017 -2686.73969232137 Force two-norm initial, final = 402.57071 0.15989330 Force max component initial, final = 131.83526 0.023371161 Final line search alpha, max atom move = 1.0000000 0.023371161 Iterations, force evaluations = 78 136 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.1059 | 2.1059 | 2.1059 | 0.0 | 95.84 Neigh | 0.057242 | 0.057242 | 0.057242 | 0.0 | 2.61 Comm | 0.019997 | 0.019997 | 0.019997 | 0.0 | 0.91 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01406 | | | 0.64 Nlocal: 606.000 ave 606 max 606 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5858.00 ave 5858 max 5858 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: 135664.0 ave 135664 max 135664 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 135664 Ave neighs/atom = 223.86799 Neighbor list builds = 3 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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 4 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4527 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 78 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.954 | 4.954 | 4.954 Mbytes Step Temp E_pair E_mol TotEng Press Volume 78 0 -2686.7397 0 -2686.7397 2450.2429 6629.3596 81 0 -2686.7676 0 -2686.7676 -385.7328 6639.9732 Loop time of 0.0790678 on 1 procs for 3 steps with 606 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 = -2686.73969232137 -2686.76656444215 -2686.76760473067 Force two-norm initial, final = 23.794929 3.1165801 Force max component initial, final = 21.019365 2.3382701 Final line search alpha, max atom move = 0.00026120057 0.00061075748 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.076674 | 0.076674 | 0.076674 | 0.0 | 96.97 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00062931 | 0.00062931 | 0.00062931 | 0.0 | 0.80 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001764 | | | 2.23 Nlocal: 606.000 ave 606 max 606 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5858.00 ave 5858 max 5858 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: 135620.0 ave 135620 max 135620 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 135620 Ave neighs/atom = 223.79538 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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 4 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4527 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) = 5.092 | 5.092 | 5.092 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2686.7676 0 -2686.7676 -385.7328 Loop time of 6.556e-06 on 1 procs for 0 steps with 606 atoms 152.5% 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 | | 6.556e-06 | | |100.00 Nlocal: 606.000 ave 606 max 606 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5858.00 ave 5858 max 5858 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: 135556.0 ave 135556 max 135556 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 135556 Ave neighs/atom = 223.68977 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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 4 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4527 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) = 5.092 | 5.092 | 5.092 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 -2686.7676 -2686.7676 15.327781 87.007706 4.9788531 -385.7328 -385.7328 -563.63575 -111.08024 -482.4824 2.3143072 397.25536 Loop time of 6.816e-06 on 1 procs for 0 steps with 606 atoms 249.4% 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 | | 6.816e-06 | | |100.00 Nlocal: 606.000 ave 606 max 606 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5858.00 ave 5858 max 5858 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 67778.0 ave 67778 max 67778 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 135556.0 ave 135556 max 135556 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 135556 Ave neighs/atom = 223.68977 Neighbor list builds = 0 Dangerous builds = 0 606 -2686.76760473067 eV 2.31430722899673 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02