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 = 3.0829274 3.0829274 3.0829274 Created orthogonal box = (0.0000000 -56.849455 0.0000000) to (28.423186 56.849455 3.0829274) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.3470755 4.3470755 3.0829274 Created 341 atoms using lattice units in orthogonal box = (0.0000000 -56.849455 0.0000000) to (28.423186 56.849455 3.0829274) create_atoms CPU = 0.000 seconds 341 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.3470755 4.3470755 3.0829274 Created 341 atoms using lattice units in orthogonal box = (0.0000000 -56.849455 0.0000000) to (28.423186 56.849455 3.0829274) create_atoms CPU = 0.000 seconds 341 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 9 35 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, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 10 atoms, new total = 672 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_152208847456_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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 9 35 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 5.678 | 5.678 | 5.678 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4289.4742 0 -4289.4742 12274.053 137 0 -4362.702 0 -4362.702 -21891.806 Loop time of 20.2717 on 1 procs for 137 steps with 672 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 = -4289.47419555766 -4362.6980692489 -4362.70199211447 Force two-norm initial, final = 168.68006 0.28254099 Force max component initial, final = 82.397877 0.075957706 Final line search alpha, max atom move = 1.0000000 0.075957706 Iterations, force evaluations = 137 258 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 20.246 | 20.246 | 20.246 | 0.0 | 99.87 Neigh | 0.011958 | 0.011958 | 0.011958 | 0.0 | 0.06 Comm | 0.0091797 | 0.0091797 | 0.0091797 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004398 | | | 0.02 Nlocal: 672.000 ave 672 max 672 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5409.00 ave 5409 max 5409 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: 48198.0 ave 48198 max 48198 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 48198 Ave neighs/atom = 71.723214 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 9 35 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 137 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.679 | 5.679 | 5.679 Mbytes Step Temp E_pair E_mol TotEng Press Volume 137 0 -4362.702 0 -4362.702 -21891.806 9963.051 150 0 -4363.6047 0 -4363.6047 722.20349 9851.8279 Loop time of 1.06845 on 1 procs for 13 steps with 672 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 = -4362.70199211446 -4363.60365491675 -4363.60472510978 Force two-norm initial, final = 192.88236 0.78953100 Force max component initial, final = 155.17331 0.33007425 Final line search alpha, max atom move = 0.00034272051 0.00011312322 Iterations, force evaluations = 13 14 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0669 | 1.0669 | 1.0669 | 0.0 | 99.85 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0003837 | 0.0003837 | 0.0003837 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001204 | | | 0.11 Nlocal: 672.000 ave 672 max 672 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5414.00 ave 5414 max 5414 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: 48258.0 ave 48258 max 48258 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 48258 Ave neighs/atom = 71.812500 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 9 35 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/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) = 5.817 | 5.817 | 5.817 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4363.6047 0 -4363.6047 722.20349 Loop time of 1.9e-06 on 1 procs for 0 steps with 672 atoms 157.9% 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 | | 1.9e-06 | | |100.00 Nlocal: 672.000 ave 672 max 672 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5414.00 ave 5414 max 5414 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: 49752.0 ave 49752 max 49752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 49752 Ave neighs/atom = 74.035714 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 9 35 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/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) = 5.817 | 5.817 | 5.817 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 -4363.6047 -4363.6047 28.461652 113.69891 3.0443909 722.20349 722.20349 50.054618 2063.5477 53.008109 2.5745571 899.73669 Loop time of 2.2e-06 on 1 procs for 0 steps with 672 atoms 181.8% 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 | | 2.2e-06 | | |100.00 Nlocal: 672.000 ave 672 max 672 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5414.00 ave 5414 max 5414 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 24876.0 ave 24876 max 24876 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 49752.0 ave 49752 max 49752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 49752 Ave neighs/atom = 74.035714 Neighbor list builds = 0 Dangerous builds = 0 672 -4363.60472510978 eV 2.57455714779971 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:21