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 = 3.5162328 3.5162328 3.5162328 Created orthogonal box = (0.0000000 -44.754337 0.0000000) to (31.646095 44.754337 4.9727041) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8603880 6.0777495 4.9727041 Created 648 atoms using lattice units in orthogonal box = (0.0000000 -44.754337 0.0000000) to (31.646095 44.754337 4.9727041) create_atoms CPU = 0.002 seconds 648 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8603880 6.0777495 4.9727041 Created 650 atoms using lattice units in orthogonal box = (0.0000000 -44.754337 0.0000000) to (31.646095 44.754337 4.9727041) create_atoms CPU = 0.001 seconds 650 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 = 8.9 ghost atom cutoff = 8.9 binsize = 4.45, bins = 8 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 8.9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1298 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_047308317761_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 = 8.9 ghost atom cutoff = 8.9 binsize = 4.45, bins = 8 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.9 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) = 5.902 | 5.902 | 5.902 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5444.8897 0 -5444.8897 160272.99 80 0 -6316.8217 0 -6316.8217 4840.9988 Loop time of 2.92908 on 1 procs for 80 steps with 1298 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 = -5444.8896863288 -6316.81579689156 -6316.82172588628 Force two-norm initial, final = 1905.0775 0.28279273 Force max component initial, final = 801.11336 0.045954318 Final line search alpha, max atom move = 1.0000000 0.045954318 Iterations, force evaluations = 80 149 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.8817 | 2.8817 | 2.8817 | 0.0 | 98.38 Neigh | 0.01875 | 0.01875 | 0.01875 | 0.0 | 0.64 Comm | 0.0165 | 0.0165 | 0.0165 | 0.0 | 0.56 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0121 | | | 0.41 Nlocal: 1298.00 ave 1298 max 1298 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10052.0 ave 10052 max 10052 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: 339532.0 ave 339532 max 339532 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 339532 Ave neighs/atom = 261.58089 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 = 8.9 ghost atom cutoff = 8.9 binsize = 4.45, bins = 8 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 80 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.898 | 5.898 | 5.898 Mbytes Step Temp E_pair E_mol TotEng Press Volume 80 0 -6316.8217 0 -6316.8217 4840.9988 14085.682 84 0 -6316.9504 0 -6316.9504 -12.162104 14122.911 Loop time of 0.138852 on 1 procs for 4 steps with 1298 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 = -6316.82172588629 -6316.95018904419 -6316.95039290118 Force two-norm initial, final = 92.541653 0.70207419 Force max component initial, final = 78.849998 0.60451382 Final line search alpha, max atom move = 0.00026760120 0.00016176863 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.13594 | 0.13594 | 0.13594 | 0.0 | 97.90 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00052534 | 0.00052534 | 0.00052534 | 0.0 | 0.38 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002384 | | | 1.72 Nlocal: 1298.00 ave 1298 max 1298 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9745.00 ave 9745 max 9745 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: 340028.0 ave 340028 max 340028 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 340028 Ave neighs/atom = 261.96302 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 = 8.9 ghost atom cutoff = 8.9 binsize = 4.45, bins = 8 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.9 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) = 6.036 | 6.036 | 6.036 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6316.9504 0 -6316.9504 -12.162104 Loop time of 2.077e-06 on 1 procs for 0 steps with 1298 atoms 192.6% 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 | | 2.077e-06 | | |100.00 Nlocal: 1298.00 ave 1298 max 1298 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9690.00 ave 9690 max 9690 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: 338672.0 ave 338672 max 338672 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 338672 Ave neighs/atom = 260.91834 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 = 8.9 ghost atom cutoff = 8.9 binsize = 4.45, bins = 8 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.9 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) = 6.036 | 6.036 | 6.036 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 -6316.9504 -6316.9504 31.72933 89.414037 4.9780312 -12.162104 -12.162104 17.307733 14.858615 -68.652661 2.3295367 715.3264 Loop time of 2.19e-06 on 1 procs for 0 steps with 1298 atoms 228.3% 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 | | 2.19e-06 | | |100.00 Nlocal: 1298.00 ave 1298 max 1298 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9690.00 ave 9690 max 9690 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 169336.0 ave 169336 max 169336 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 338672.0 ave 338672 max 338672 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 338672 Ave neighs/atom = 260.91834 Neighbor list builds = 0 Dangerous builds = 0 1298 -6316.95039290118 eV 2.3295367402121 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03