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 = 3.1692585 3.1692585 3.1692585 Created orthogonal box = (0.0000000 -33.838421 0.0000000) to (19.536621 33.838421 5.4893167) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1412162 4.7492520 5.4893167 Created 228 atoms using lattice units in orthogonal box = (0.0000000 -33.838421 0.0000000) to (19.536621 33.838421 5.4893167) create_atoms CPU = 0.001 seconds 228 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1412162 4.7492520 5.4893167 Created 230 atoms using lattice units in orthogonal box = (0.0000000 -33.838421 0.0000000) to (19.536621 33.838421 5.4893167) create_atoms CPU = 0.001 seconds 230 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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 6 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 6.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 458 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_014123846623_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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 6 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.6 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) = 4.457 | 4.457 | 4.457 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4815.7668 0 -4815.7668 52475.25 37 0 -4943.1796 0 -4943.1796 24259.427 Loop time of 10.4457 on 1 procs for 37 steps with 458 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 = -4815.76680994376 -4943.1751813787 -4943.17962608515 Force two-norm initial, final = 178.48050 0.23167416 Force max component initial, final = 58.462797 0.048060716 Final line search alpha, max atom move = 1.0000000 0.048060716 Iterations, force evaluations = 37 66 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 10.437 | 10.437 | 10.437 | 0.0 | 99.92 Neigh | 0.0025778 | 0.0025778 | 0.0025778 | 0.0 | 0.02 Comm | 0.0030487 | 0.0030487 | 0.0030487 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002984 | | | 0.03 Nlocal: 458.000 ave 458 max 458 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2727.00 ave 2727 max 2727 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: 29664.0 ave 29664 max 29664 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29664 Ave neighs/atom = 64.768559 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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 6 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 37 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.456 | 4.456 | 4.456 Mbytes Step Temp E_pair E_mol TotEng Press Volume 37 0 -4943.1796 0 -4943.1796 24259.427 7257.8474 46 0 -4943.9089 0 -4943.9089 -241.8025 7324.4127 Loop time of 1.5983 on 1 procs for 9 steps with 458 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4943.17962608515 -4943.908561471 -4943.90888834497 Force two-norm initial, final = 202.50508 2.1360843 Force max component initial, final = 162.52459 1.5375877 Final line search alpha, max atom move = 0.00033701100 0.00051818398 Iterations, force evaluations = 9 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.5967 | 1.5967 | 1.5967 | 0.0 | 99.90 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00029137 | 0.00029137 | 0.00029137 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001351 | | | 0.08 Nlocal: 458.000 ave 458 max 458 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2657.00 ave 2657 max 2657 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: 29640.0 ave 29640 max 29640 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29640 Ave neighs/atom = 64.716157 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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 6 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.6 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) = 4.594 | 4.594 | 4.594 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4943.9089 0 -4943.9089 -241.8025 Loop time of 1.385e-06 on 1 procs for 0 steps with 458 atoms 144.4% 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 | | 1.385e-06 | | |100.00 Nlocal: 458.000 ave 458 max 458 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2640.00 ave 2640 max 2640 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: 29560.0 ave 29560 max 29560 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29560 Ave neighs/atom = 64.541485 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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 6 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.6 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) = 4.594 | 4.594 | 4.594 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 -4943.9089 -4943.9089 19.51437 68.232033 5.500852 -241.8025 -241.8025 -335.95609 -90.775611 -298.6758 2.5118804 353.15095 Loop time of 1.4e-06 on 1 procs for 0 steps with 458 atoms 142.9% 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 | | 1.4e-06 | | |100.00 Nlocal: 458.000 ave 458 max 458 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2640.00 ave 2640 max 2640 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 14780.0 ave 14780 max 14780 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 29560.0 ave 29560 max 29560 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29560 Ave neighs/atom = 64.541485 Neighbor list builds = 0 Dangerous builds = 0 458 -2491.49948069912 eV 2.51188043251656 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:12