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 = 4.0499990 4.0499990 4.0499990 Created orthogonal box = (0.0000000 -51.865294 0.0000000) to (25.932647 51.865294 4.0499990) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6925322 5.6925322 4.0499990 Created 327 atoms using lattice units in orthogonal box = (0.0000000 -51.865294 0.0000000) to (25.932647 51.865294 4.0499990) create_atoms CPU = 0.001 seconds 327 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6925322 5.6925322 4.0499990 Created 329 atoms using lattice units in orthogonal box = (0.0000000 -51.865294 0.0000000) to (25.932647 51.865294 4.0499990) create_atoms CPU = 0.000 seconds 329 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 ghost atom cutoff = 8 binsize = 4, bins = 7 26 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 656 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_093637366498_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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 7 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 4.532 | 4.532 | 4.532 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1899.9977 0 -1899.9977 55395.474 128 0 -2198.717 0 -2198.717 2631.4287 Loop time of 12.3273 on 1 procs for 128 steps with 656 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1899.99770795028 -2198.71554169338 -2198.71704969734 Force two-norm initial, final = 410.36838 0.11064577 Force max component initial, final = 131.74653 0.033157163 Final line search alpha, max atom move = 1.0000000 0.033157163 Iterations, force evaluations = 128 222 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 12.283 | 12.283 | 12.283 | 0.0 | 99.64 Neigh | 0.016603 | 0.016603 | 0.016603 | 0.0 | 0.13 Comm | 0.015211 | 0.015211 | 0.015211 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01269 | | | 0.10 Nlocal: 656.000 ave 656 max 656 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5313.00 ave 5313 max 5313 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: 87718.0 ave 87718 max 87718 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 87718 Ave neighs/atom = 133.71646 Neighbor list builds = 3 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 ghost atom cutoff = 8 binsize = 4, bins = 7 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 128 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.527 | 4.527 | 4.527 Mbytes Step Temp E_pair E_mol TotEng Press Volume 128 0 -2198.717 0 -2198.717 2631.4287 10894.532 134 0 -2198.8018 0 -2198.8018 40.538817 10929.394 Loop time of 0.404768 on 1 procs for 6 steps with 656 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 = -2198.71704969734 -2198.80162563786 -2198.80178027695 Force two-norm initial, final = 37.990374 0.50509479 Force max component initial, final = 35.614085 0.32340864 Final line search alpha, max atom move = 0.0011259600 0.00036414517 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.40296 | 0.40296 | 0.40296 | 0.0 | 99.55 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00033146 | 0.00033146 | 0.00033146 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001478 | | | 0.37 Nlocal: 656.000 ave 656 max 656 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4836.00 ave 4836 max 4836 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: 87668.0 ave 87668 max 87668 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 87668 Ave neighs/atom = 133.64024 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 ghost atom cutoff = 8 binsize = 4, bins = 7 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 4.665 | 4.665 | 4.665 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2198.8018 0 -2198.8018 40.538817 Loop time of 7.795e-06 on 1 procs for 0 steps with 656 atoms 141.1% 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 | | 7.795e-06 | | |100.00 Nlocal: 656.000 ave 656 max 656 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4823.00 ave 4823 max 4823 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: 87616.0 ave 87616 max 87616 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 87616 Ave neighs/atom = 133.56098 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 ghost atom cutoff = 8 binsize = 4, bins = 7 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 4.665 | 4.665 | 4.665 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 -2198.8018 -2198.8018 25.927531 104.26638 4.0428778 40.538817 40.538817 47.400203 42.729938 31.48631 2.5651517 185.69603 Loop time of 2.512e-06 on 1 procs for 0 steps with 656 atoms 159.2% 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 | | 2.512e-06 | | |100.00 Nlocal: 656.000 ave 656 max 656 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4823.00 ave 4823 max 4823 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 43808.0 ave 43808 max 43808 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 87616.0 ave 87616 max 87616 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 87616 Ave neighs/atom = 133.56098 Neighbor list builds = 0 Dangerous builds = 0 656 -2198.80178027695 eV 2.56515165693667 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:13