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 = 3.6073527 3.6073527 3.6073527 Created orthogonal box = (0.0000000 -52.523848 0.0000000) to (26.261924 52.523848 3.6073527) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.4595720 4.4595720 3.6073527 Created 424 atoms using lattice units in orthogonal box = (0.0000000 -52.523848 0.0000000) to (26.261924 52.523848 3.6073527) create_atoms CPU = 0.001 seconds 424 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.4595720 4.4595720 3.6073527 Created 426 atoms using lattice units in orthogonal box = (0.0000000 -52.523848 0.0000000) to (26.261924 52.523848 3.6073527) create_atoms CPU = 0.000 seconds 426 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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 5 18 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 12.1544 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 848 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_151002396060_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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 5 18 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.1544 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) = 6.655 | 6.655 | 6.655 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2731.1979 0 -2731.1979 47587.006 47 0 -2977.6929 0 -2977.6929 6738.3049 Loop time of 2.12949 on 1 procs for 47 steps with 848 atoms 99.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2731.19791951105 -2977.69055604169 -2977.69293923429 Force two-norm initial, final = 380.56100 0.18259941 Force max component initial, final = 108.46454 0.037060051 Final line search alpha, max atom move = 1.0000000 0.037060051 Iterations, force evaluations = 47 80 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.0819 | 2.0819 | 2.0819 | 0.0 | 97.77 Neigh | 0.026979 | 0.026979 | 0.026979 | 0.0 | 1.27 Comm | 0.014024 | 0.014024 | 0.014024 | 0.0 | 0.66 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006554 | | | 0.31 Nlocal: 848.000 ave 848 max 848 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14220.0 ave 14220 max 14220 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: 532980.0 ave 532980 max 532980 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 532980 Ave neighs/atom = 628.51415 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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 5 18 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.1544 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 47 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.654 | 6.654 | 6.654 Mbytes Step Temp E_pair E_mol TotEng Press Volume 47 0 -2977.6929 0 -2977.6929 6738.3049 9951.801 53 0 -2977.8798 0 -2977.8798 -239.03269 10001.58 Loop time of 0.206459 on 1 procs for 6 steps with 848 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 = -2977.6929392343 -2977.87898459711 -2977.87981906647 Force two-norm initial, final = 80.033902 3.3005108 Force max component initial, final = 66.595500 2.5918115 Final line search alpha, max atom move = 0.00021529653 0.00055800802 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.20175 | 0.20175 | 0.20175 | 0.0 | 97.72 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00094731 | 0.00094731 | 0.00094731 | 0.0 | 0.46 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003757 | | | 1.82 Nlocal: 848.000 ave 848 max 848 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14159.0 ave 14159 max 14159 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: 531556.0 ave 531556 max 531556 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 531556 Ave neighs/atom = 626.83491 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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 5 18 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.1544 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) = 6.792 | 6.792 | 6.792 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2977.8798 0 -2977.8798 -239.03269 Loop time of 2.516e-06 on 1 procs for 0 steps with 848 atoms 159.0% 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 | | 2.516e-06 | | |100.00 Nlocal: 848.000 ave 848 max 848 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14228.0 ave 14228 max 14228 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: 530200.0 ave 530200 max 530200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 530200 Ave neighs/atom = 625.23585 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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 5 18 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.1544 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) = 6.792 | 6.792 | 6.792 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 -2977.8798 -2977.8798 26.220743 105.59906 3.6121314 -239.03269 -239.03269 -414.5373 20.728052 -323.28881 2.2870059 377.48623 Loop time of 2.489e-06 on 1 procs for 0 steps with 848 atoms 281.2% 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 | | 2.489e-06 | | |100.00 Nlocal: 848.000 ave 848 max 848 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14228.0 ave 14228 max 14228 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 265100.0 ave 265100 max 265100 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 530200.0 ave 530200 max 530200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 530200 Ave neighs/atom = 625.23585 Neighbor list builds = 0 Dangerous builds = 0 848 -2977.87981906647 eV 2.2870058673844 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02