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 = 3.5200000 3.5200000 3.5200000 Created orthogonal box = (0.0000000 -62.175597 0.0000000) to (35.897098 62.175597 6.0968189) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5226304 5.5798613 6.0968189 Created 1246 atoms using lattice units in orthogonal box = (0.0000000 -62.175597 0.0000000) to (35.897098 62.175597 6.0968189) create_atoms CPU = 0.003 seconds 1246 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5226304 5.5798613 6.0968189 Created 1250 atoms using lattice units in orthogonal box = (0.0000000 -62.175597 0.0000000) to (35.897098 62.175597 6.0968189) create_atoms CPU = 0.003 seconds 1250 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 9 30 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 2492 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_103383163946_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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 9 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 10.84 | 10.84 | 10.84 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10247.04 0 -10247.04 94999.781 89 0 -11051.801 0 -11051.801 3693.1012 Loop time of 4.15606 on 1 procs for 89 steps with 2492 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 = -10247.0404063813 -11051.790013539 -11051.8007923075 Force two-norm initial, final = 2295.9398 0.36552065 Force max component initial, final = 671.77860 0.071546339 Final line search alpha, max atom move = 1.0000000 0.071546339 Iterations, force evaluations = 89 150 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.0404 | 4.0404 | 4.0404 | 0.0 | 97.22 Neigh | 0.067589 | 0.067589 | 0.067589 | 0.0 | 1.63 Comm | 0.026299 | 0.026299 | 0.026299 | 0.0 | 0.63 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02173 | | | 0.52 Nlocal: 2492.00 ave 2492 max 2492 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14152.0 ave 14152 max 14152 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: 559462.0 ave 559462 max 559462 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 559462 Ave neighs/atom = 224.50321 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 9 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 89 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 10.84 | 10.84 | 10.84 Mbytes Step Temp E_pair E_mol TotEng Press Volume 89 0 -11051.801 0 -11051.801 3693.1012 27215.266 93 0 -11051.992 0 -11051.992 -4.2898198 27271.395 Loop time of 0.204852 on 1 procs for 4 steps with 2492 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 = -11051.8007923075 -11051.9906104605 -11051.991565572 Force two-norm initial, final = 142.86051 0.79496807 Force max component initial, final = 135.02014 0.45443158 Final line search alpha, max atom move = 8.7706375e-05 3.9856546e-05 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.19991 | 0.19991 | 0.19991 | 0.0 | 97.59 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00081493 | 0.00081493 | 0.00081493 | 0.0 | 0.40 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004129 | | | 2.02 Nlocal: 2492.00 ave 2492 max 2492 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13668.0 ave 13668 max 13668 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: 559248.0 ave 559248 max 559248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 559248 Ave neighs/atom = 224.41734 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 9 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 10.35 | 10.35 | 10.35 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11051.992 0 -11051.992 -4.2898198 Loop time of 2.216e-06 on 1 procs for 0 steps with 2492 atoms 180.5% 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 | | 2.216e-06 | | |100.00 Nlocal: 2492.00 ave 2492 max 2492 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13661.0 ave 13661 max 13661 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: 558964.0 ave 558964 max 558964 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 558964 Ave neighs/atom = 224.30337 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 9 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 10.35 | 10.35 | 10.35 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 -11051.992 -11051.992 35.86134 124.69913 6.0984213 -4.2898198 -4.2898198 -24.273191 -15.300841 26.704573 2.1941169 1027.6854 Loop time of 2.266e-06 on 1 procs for 0 steps with 2492 atoms 353.0% 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 | | 2.266e-06 | | |100.00 Nlocal: 2492.00 ave 2492 max 2492 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13661.0 ave 13661 max 13661 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 279482.0 ave 279482 max 279482 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 558964.0 ave 558964 max 558964 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 558964 Ave neighs/atom = 224.30337 Neighbor list builds = 0 Dangerous builds = 0 2492 -10984.1311251032 eV 2.19411690635518 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05