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 = 3.5224675 3.5224675 3.5224675 Created orthogonal box = (0.0000000 -42.562136 0.0000000) to (52.127758 42.562136 8.6282479) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9985522 5.2473867 5.7521653 Created 1750 atoms using lattice units in orthogonal box = (0.0000000 -42.562136 0.0000000) to (52.127758 42.562136 8.6282479) create_atoms CPU = 0.003 seconds 1750 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9985522 5.2473867 5.7521653 Created 1756 atoms using lattice units in orthogonal box = (0.0000000 -42.562136 0.0000000) to (52.127758 42.562136 8.6282479) create_atoms CPU = 0.002 seconds 1756 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 = 7.18 ghost atom cutoff = 7.18 binsize = 3.59, bins = 15 24 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 7.18 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 26 atoms, new total = 3480 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_763197941039_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 = 7.18 ghost atom cutoff = 7.18 binsize = 3.59, bins = 15 24 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.18 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) = 6.571 | 6.571 | 6.571 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13211.764 0 -13211.764 142583.06 79 0 -15430.044 0 -15430.044 3313.2522 Loop time of 3.12729 on 1 procs for 79 steps with 3480 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 = -13211.7641634827 -15430.030645718 -15430.0438100075 Force two-norm initial, final = 2502.4125 0.56474330 Force max component initial, final = 409.04081 0.10460849 Final line search alpha, max atom move = 1.0000000 0.10460849 Iterations, force evaluations = 79 141 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.0211 | 3.0211 | 3.0211 | 0.0 | 96.60 Neigh | 0.065919 | 0.065919 | 0.065919 | 0.0 | 2.11 Comm | 0.015615 | 0.015615 | 0.015615 | 0.0 | 0.50 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02466 | | | 0.79 Nlocal: 3480.00 ave 3480 max 3480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10359.0 ave 10359 max 10359 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: 484584.0 ave 484584 max 484584 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 484584 Ave neighs/atom = 139.24828 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 = 7.18 ghost atom cutoff = 7.18 binsize = 3.59, bins = 15 24 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.18 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 79 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.571 | 6.571 | 6.571 Mbytes Step Temp E_pair E_mol TotEng Press Volume 79 0 -15430.044 0 -15430.044 3313.2522 38286.448 82 0 -15430.15 0 -15430.15 -4.6579342 38355.408 Loop time of 0.156569 on 1 procs for 3 steps with 3480 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 = -15430.0438100076 -15430.1497488593 -15430.1498802277 Force two-norm initial, final = 146.82515 0.64637335 Force max component initial, final = 103.48614 0.18225919 Final line search alpha, max atom move = 0.00039402140 7.1814019e-05 Iterations, force evaluations = 3 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.15196 | 0.15196 | 0.15196 | 0.0 | 97.06 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00062912 | 0.00062912 | 0.00062912 | 0.0 | 0.40 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00398 | | | 2.54 Nlocal: 3480.00 ave 3480 max 3480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10319.0 ave 10319 max 10319 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: 484620.0 ave 484620 max 484620 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 484620 Ave neighs/atom = 139.25862 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 = 7.18 ghost atom cutoff = 7.18 binsize = 3.59, bins = 15 24 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.18 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) = 6.709 | 6.709 | 6.709 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15430.15 0 -15430.15 -4.6579342 Loop time of 2.168e-06 on 1 procs for 0 steps with 3480 atoms 184.5% 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 | | 2.168e-06 | | |100.00 Nlocal: 3480.00 ave 3480 max 3480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10311.0 ave 10311 max 10311 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: 484548.0 ave 484548 max 484548 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 484548 Ave neighs/atom = 139.23793 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 = 7.18 ghost atom cutoff = 7.18 binsize = 3.59, bins = 15 24 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.18 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) = 6.709 | 6.709 | 6.709 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 -15430.15 -15430.15 52.188873 85.080705 8.6380876 -4.6579342 -4.6579342 -7.62223 -6.1006652 -0.2509074 2.3552402 1516.5671 Loop time of 2.68e-06 on 1 procs for 0 steps with 3480 atoms 261.2% 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 | | 2.68e-06 | | |100.00 Nlocal: 3480.00 ave 3480 max 3480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10311.0 ave 10311 max 10311 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 242274.0 ave 242274 max 242274 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 484548.0 ave 484548 max 484548 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 484548 Ave neighs/atom = 139.23793 Neighbor list builds = 0 Dangerous builds = 0 3480 -15430.1498802277 eV 2.35524023659022 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05