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 -61.815585 0.0000000) to (35.687464 61.815585 5.3397869) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.7938385 4.9203981 5.3397869 Created 806 atoms using lattice units in orthogonal box = (0.0000000 -61.815585 0.0000000) to (35.687464 61.815585 5.3397869) create_atoms CPU = 0.001 seconds 806 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.7938385 4.9203981 5.3397869 Created 806 atoms using lattice units in orthogonal box = (0.0000000 -61.815585 0.0000000) to (35.687464 61.815585 5.3397869) create_atoms CPU = 0.001 seconds 806 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 = 11 38 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, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 4 atoms, new total = 1608 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 = 11 38 2 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) = 6.263 | 6.263 | 6.263 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10151.905 0 -10151.905 47050.479 126 0 -10439.182 0 -10439.182 3450.214 Loop time of 50.4546 on 1 procs for 126 steps with 1608 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 = -10151.9052787766 -10439.1722089431 -10439.1815378068 Force two-norm initial, final = 339.52734 0.48732374 Force max component initial, final = 85.868202 0.12633526 Final line search alpha, max atom move = 0.57523744 0.072672770 Iterations, force evaluations = 126 242 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 50.409 | 50.409 | 50.409 | 0.0 | 99.91 Neigh | 0.024307 | 0.024307 | 0.024307 | 0.0 | 0.05 Comm | 0.012104 | 0.012104 | 0.012104 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00894 | | | 0.02 Nlocal: 1608.00 ave 1608 max 1608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6969.00 ave 6969 max 6969 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: 119982.0 ave 119982 max 119982 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 119982 Ave neighs/atom = 74.615672 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 = 11 38 2 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 : 126 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.645 | 6.645 | 6.645 Mbytes Step Temp E_pair E_mol TotEng Press Volume 126 0 -10439.182 0 -10439.182 3450.214 23559.583 132 0 -10440.022 0 -10440.022 878.21524 23585.706 Loop time of 1.79022 on 1 procs for 6 steps with 1608 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 = -10439.1815378068 -10440.0215384813 -10440.0215832039 Force two-norm initial, final = 282.49455 2.1722486 Force max component initial, final = 252.34913 1.3399052 Final line search alpha, max atom move = 0.0016225453 0.0021740569 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.7887 | 1.7887 | 1.7887 | 0.0 | 99.91 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0003688 | 0.0003688 | 0.0003688 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001175 | | | 0.07 Nlocal: 1608.00 ave 1608 max 1608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6962.00 ave 6962 max 6962 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: 117580.0 ave 117580 max 117580 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 117580 Ave neighs/atom = 73.121891 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 = 11 38 2 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) = 6.782 | 6.782 | 6.782 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10440.022 0 -10440.022 878.21524 Loop time of 2e-06 on 1 procs for 0 steps with 1608 atoms 100.0% 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 | | 2e-06 | | |100.00 Nlocal: 1608.00 ave 1608 max 1608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6930.00 ave 6930 max 6930 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: 117922.0 ave 117922 max 117922 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 117922 Ave neighs/atom = 73.334577 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 = 11 38 2 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) = 6.782 | 6.782 | 6.782 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 -10440.022 -10440.022 35.555067 123.63117 5.3656138 878.21524 878.21524 80.931309 2462.2544 91.459969 2.5056664 2615.1661 Loop time of 2.5e-06 on 1 procs for 0 steps with 1608 atoms 200.0% 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 | | 2.5e-06 | | |100.00 Nlocal: 1608.00 ave 1608 max 1608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6930.00 ave 6930 max 6930 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 58961.0 ave 58961 max 58961 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 117922.0 ave 117922 max 117922 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 117922 Ave neighs/atom = 73.334577 Neighbor list builds = 0 Dangerous builds = 0 1608 -10440.0215832039 eV 2.50566641108183 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:53