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 = 3.6239511 3.6239511 3.6239511 Created orthogonal box = (0.0000000 -46.412842 0.0000000) to (23.204609 46.412842 3.6239511) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0936947 5.0936947 3.6239511 Created 329 atoms using lattice units in orthogonal box = (0.0000000 -46.412842 0.0000000) to (23.204609 46.412842 3.6239511) create_atoms CPU = 0.001 seconds 329 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0936947 5.0936947 3.6239511 Created 329 atoms using lattice units in orthogonal box = (0.0000000 -46.412842 0.0000000) to (23.204609 46.412842 3.6239511) create_atoms CPU = 0.000 seconds 329 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 = 7 27 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 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 652 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_427873955970_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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 7 27 2 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) = 4.522 | 4.522 | 4.522 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2699.9902 0 -2699.9902 7993.1474 62 0 -2725.5548 0 -2725.5548 -7879.7754 Loop time of 4.78924 on 1 procs for 62 steps with 652 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 = -2699.99022817069 -2725.5522450976 -2725.55482243158 Force two-norm initial, final = 23.004407 0.16193182 Force max component initial, final = 6.5855813 0.054498343 Final line search alpha, max atom move = 1.0000000 0.054498343 Iterations, force evaluations = 62 106 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.773 | 4.773 | 4.773 | 0.0 | 99.66 Neigh | 0.0051807 | 0.0051807 | 0.0051807 | 0.0 | 0.11 Comm | 0.0058696 | 0.0058696 | 0.0058696 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005169 | | | 0.11 Nlocal: 652.000 ave 652 max 652 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4766.00 ave 4766 max 4766 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: 86224.0 ave 86224 max 86224 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 86224 Ave neighs/atom = 132.24540 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 = 7 27 2 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 : 62 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.522 | 4.522 | 4.522 Mbytes Step Temp E_pair E_mol TotEng Press Volume 62 0 -2725.5548 0 -2725.5548 -7879.7754 7805.9316 117 0 -2728.7675 0 -2728.7675 -16328.131 7844.3946 Loop time of 2.81044 on 1 procs for 55 steps with 652 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 = -2725.55482243157 -2728.76543518794 -2728.76748547841 Force two-norm initial, final = 98.407170 2.9005638 Force max component initial, final = 76.591897 1.7552136 Final line search alpha, max atom move = 0.00014869752 0.00026099590 Iterations, force evaluations = 55 61 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.7941 | 2.7941 | 2.7941 | 0.0 | 99.42 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0026143 | 0.0026143 | 0.0026143 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01369 | | | 0.49 Nlocal: 652.000 ave 652 max 652 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4769.00 ave 4769 max 4769 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: 86194.0 ave 86194 max 86194 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 86194 Ave neighs/atom = 132.19939 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 = 7 27 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) = 4.661 | 4.661 | 4.661 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2728.7675 0 -2728.7675 -16328.131 Loop time of 2.345e-06 on 1 procs for 0 steps with 652 atoms 170.6% 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 | | 2.345e-06 | | |100.00 Nlocal: 652.000 ave 652 max 652 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4841.00 ave 4841 max 4841 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: 85210.0 ave 85210 max 85210 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 85210 Ave neighs/atom = 130.69018 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 = 7 27 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) = 4.661 | 4.661 | 4.661 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 -2728.7675 -2728.7675 22.554532 92.825684 3.7467737 -16328.131 -16328.131 348.44998 -49554.815 221.97186 2.3526881 232.92774 Loop time of 2.222e-06 on 1 procs for 0 steps with 652 atoms 180.0% 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 | | 2.222e-06 | | |100.00 Nlocal: 652.000 ave 652 max 652 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4841.00 ave 4841 max 4841 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 42605.0 ave 42605 max 42605 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 85210.0 ave 85210 max 85210 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 85210 Ave neighs/atom = 130.69018 Neighbor list builds = 0 Dangerous builds = 0 652 -2728.76748547841 eV 2.35268814609587 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08