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 -37.757995 0.0000000) to (5.3397869 37.757995 4.3599177) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3397869 5.0343993 4.3599177 Created 60 atoms using lattice units in orthogonal box = (0.0000000 -37.757995 0.0000000) to (5.3397869 37.757995 4.3599177) create_atoms CPU = 0.001 seconds 60 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.3397869 5.0343993 4.3599177 Created 62 atoms using lattice units in orthogonal box = (0.0000000 -37.757995 0.0000000) to (5.3397869 37.757995 4.3599177) create_atoms CPU = 0.000 seconds 62 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 = 2 23 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 2 atoms, new total = 120 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_001#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 = 2 23 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) = 4.779 | 4.779 | 4.779 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -777.51002 0 -777.51002 2860.0282 44 0 -780.95481 0 -780.95481 -2210.106 Loop time of 3.0361 on 1 procs for 44 steps with 120 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 = -777.510019262173 -780.954233046463 -780.954808980415 Force two-norm initial, final = 3.8486800 0.10892536 Force max component initial, final = 1.7080585 0.022648505 Final line search alpha, max atom move = 1.0000000 0.022648505 Iterations, force evaluations = 44 87 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.0332 | 3.0332 | 3.0332 | 0.0 | 99.90 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0016752 | 0.0016752 | 0.0016752 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001244 | | | 0.04 Nlocal: 120.000 ave 120 max 120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2120.00 ave 2120 max 2120 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: 7872.00 ave 7872 max 7872 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 7872 Ave neighs/atom = 65.600000 Neighbor list builds = 0 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 = 2 23 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 : 44 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.779 | 4.779 | 4.779 Mbytes Step Temp E_pair E_mol TotEng Press Volume 44 0 -780.95481 0 -780.95481 -2210.106 1758.0901 48 0 -780.9962 0 -780.9962 -57.91663 1756.2159 Loop time of 0.209076 on 1 procs for 4 steps with 120 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 = -780.954808980414 -780.99561672287 -780.996202527048 Force two-norm initial, final = 17.672338 0.40993085 Force max component initial, final = 11.556947 0.14526114 Final line search alpha, max atom move = 0.00061572528 8.9440958e-05 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.20854 | 0.20854 | 0.20854 | 0.0 | 99.74 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00011003 | 0.00011003 | 0.00011003 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0004304 | | | 0.21 Nlocal: 120.000 ave 120 max 120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2124.00 ave 2124 max 2124 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: 8576.00 ave 8576 max 8576 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 8576 Ave neighs/atom = 71.466667 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 = 2 23 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) = 4.917 | 4.917 | 4.917 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -780.9962 0 -780.9962 -57.91663 Loop time of 1.82e-06 on 1 procs for 0 steps with 120 atoms 164.8% 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 | | 1.82e-06 | | |100.00 Nlocal: 120.000 ave 120 max 120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2112.00 ave 2112 max 2112 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: 8576.00 ave 8576 max 8576 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 8576 Ave neighs/atom = 71.466667 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 = 2 23 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) = 4.917 | 4.917 | 4.917 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 -780.9962 -780.9962 5.3583366 75.373136 4.3484184 -57.91663 -57.91663 -132.9805 89.953789 -130.72318 2.6660524 191.31056 Loop time of 2.005e-06 on 1 procs for 0 steps with 120 atoms 149.6% 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 | | 2.005e-06 | | |100.00 Nlocal: 120.000 ave 120 max 120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2112.00 ave 2112 max 2112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 4288.00 ave 4288 max 4288 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 8576.00 ave 8576 max 8576 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 8576 Ave neighs/atom = 71.466667 Neighbor list builds = 0 Dangerous builds = 0 120 -780.996202527048 eV 2.66605240796455 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03