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 = 3.1582519 3.1582519 3.1582519 Created orthogonal box = (0.0000000 -33.572679 0.0000000) to (33.572679 33.572679 3.1582519) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.4565503 4.4565503 3.1582519 Created 226 atoms using lattice units in orthogonal box = (0.0000000 -33.572679 0.0000000) to (33.572679 33.572679 3.1582519) create_atoms CPU = 0.002 seconds 226 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.4565503 4.4565503 3.1582519 Created 227 atoms using lattice units in orthogonal box = (0.0000000 -33.572679 0.0000000) to (33.572679 33.572679 3.1582519) create_atoms CPU = 0.001 seconds 227 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 = 8.48804 ghost atom cutoff = 8.48804 binsize = 4.24402, bins = 8 16 1 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 8.48804 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 1 atoms, new total = 452 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_228581001644_004#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 = 8.48804 ghost atom cutoff = 8.48804 binsize = 4.24402, bins = 8 16 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.48804 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) = 4.476 | 4.476 | 4.476 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -846.65841 0 -846.65841 504686.73 115 0 -2873.3237 0 -2873.3237 11067.316 Loop time of 1.64662 on 1 procs for 115 steps with 452 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 = -846.658405677002 -2873.32087645819 -2873.32373924848 Force two-norm initial, final = 3570.6693 0.30642291 Force max component initial, final = 1338.1453 0.027510063 Final line search alpha, max atom move = 0.88036082 0.024218782 Iterations, force evaluations = 115 211 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.588 | 1.588 | 1.588 | 0.0 | 96.44 Neigh | 0.019146 | 0.019146 | 0.019146 | 0.0 | 1.16 Comm | 0.023267 | 0.023267 | 0.023267 | 0.0 | 1.41 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01622 | | | 0.99 Nlocal: 452.000 ave 452 max 452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4666.00 ave 4666 max 4666 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: 73528.0 ave 73528 max 73528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 73528 Ave neighs/atom = 162.67257 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 = 8.48804 ghost atom cutoff = 8.48804 binsize = 4.24402, bins = 8 16 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.48804 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 115 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.473 | 4.473 | 4.473 Mbytes Step Temp E_pair E_mol TotEng Press Volume 115 0 -2873.3237 0 -2873.3237 11067.316 7119.4879 165 0 -2880.4121 0 -2880.4121 -1251.2452 7143.4304 Loop time of 0.426683 on 1 procs for 50 steps with 452 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 = -2873.32373924848 -2880.40973193573 -2880.41212648932 Force two-norm initial, final = 205.60569 10.335176 Force max component initial, final = 151.48161 5.7548485 Final line search alpha, max atom move = 0.00054661381 0.0031456797 Iterations, force evaluations = 50 51 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.39285 | 0.39285 | 0.39285 | 0.0 | 92.07 Neigh | 0.0094145 | 0.0094145 | 0.0094145 | 0.0 | 2.21 Comm | 0.0058298 | 0.0058298 | 0.0058298 | 0.0 | 1.37 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01859 | | | 4.36 Nlocal: 452.000 ave 452 max 452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5491.00 ave 5491 max 5491 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: 72940.0 ave 72940 max 72940 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 72940 Ave neighs/atom = 161.37168 Neighbor list builds = 1 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 = 8.48804 ghost atom cutoff = 8.48804 binsize = 4.24402, bins = 9 17 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.48804 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) = 4.618 | 4.618 | 4.618 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2880.4121 0 -2880.4121 -1251.2452 Loop time of 6.295e-06 on 1 procs for 0 steps with 452 atoms 174.7% 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 | | 6.295e-06 | | |100.00 Nlocal: 452.000 ave 452 max 452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5463.00 ave 5463 max 5463 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: 72556.0 ave 72556 max 72556 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 72556 Ave neighs/atom = 160.52212 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 = 8.48804 ghost atom cutoff = 8.48804 binsize = 4.24402, bins = 9 17 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.48804 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) = 4.618 | 4.618 | 4.618 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 -2880.4121 -2880.4121 34.517775 68.884532 3.0042932 -1251.2452 -1251.2452 -1267.7218 -1258.1988 -1227.8151 2.6336979 139.78907 Loop time of 6.815e-06 on 1 procs for 0 steps with 452 atoms 234.8% 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 | | 6.815e-06 | | |100.00 Nlocal: 452.000 ave 452 max 452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5463.00 ave 5463 max 5463 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 36278.0 ave 36278 max 36278 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 72556.0 ave 72556 max 72556 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 72556 Ave neighs/atom = 160.52212 Neighbor list builds = 0 Dangerous builds = 0 452 -2880.41212648932 eV 2.6336978571179 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02