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 = 4.0445274 4.0445274 4.0445274 Created orthogonal box = (0.0000000 -41.246248 0.0000000) to (20.623124 41.246248 4.0445274) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.7591824 4.7591824 4.0445274 Created 208 atoms using lattice units in orthogonal box = (0.0000000 -41.246248 0.0000000) to (20.623124 41.246248 4.0445274) create_atoms CPU = 0.001 seconds 208 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.7591824 4.7591824 4.0445274 Created 210 atoms using lattice units in orthogonal box = (0.0000000 -41.246248 0.0000000) to (20.623124 41.246248 4.0445274) create_atoms CPU = 0.001 seconds 210 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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 5 17 1 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 10 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 416 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_722733117926_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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 5 17 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10 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) = 4.879 | 4.879 | 4.879 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1341.5099 0 -1341.5099 23369.281 40 0 -1372.5472 0 -1372.5472 8688.5896 Loop time of 1.16802 on 1 procs for 40 steps with 416 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 = -1341.50986697855 -1372.54615247681 -1372.54723211722 Force two-norm initial, final = 56.155481 0.072166941 Force max component initial, final = 18.134471 0.010863695 Final line search alpha, max atom move = 1.0000000 0.010863695 Iterations, force evaluations = 40 75 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1526 | 1.1526 | 1.1526 | 0.0 | 98.68 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0092796 | 0.0092796 | 0.0092796 | 0.0 | 0.79 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006156 | | | 0.53 Nlocal: 416.000 ave 416 max 416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5170.00 ave 5170 max 5170 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: 103224.0 ave 103224 max 103224 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 103224 Ave neighs/atom = 248.13462 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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 5 17 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 40 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.879 | 4.879 | 4.879 Mbytes Step Temp E_pair E_mol TotEng Press Volume 40 0 -1372.5472 0 -1372.5472 8688.5896 6880.7641 52 0 -1372.8591 0 -1372.8591 26.255147 6944.5268 Loop time of 0.221886 on 1 procs for 12 steps with 416 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 = -1372.54723211723 -1372.85881455498 -1372.85911465216 Force two-norm initial, final = 70.994244 0.34202991 Force max component initial, final = 61.192900 0.13790150 Final line search alpha, max atom move = 0.0010754692 0.00014830882 Iterations, force evaluations = 12 13 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.21525 | 0.21525 | 0.21525 | 0.0 | 97.01 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0015774 | 0.0015774 | 0.0015774 | 0.0 | 0.71 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005057 | | | 2.28 Nlocal: 416.000 ave 416 max 416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5195.00 ave 5195 max 5195 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: 102280.0 ave 102280 max 102280 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 102280 Ave neighs/atom = 245.86538 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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 5 17 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10 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) = 5.017 | 5.017 | 5.017 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1372.8591 0 -1372.8591 26.255147 Loop time of 6.325e-06 on 1 procs for 0 steps with 416 atoms 173.9% 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 | | 6.325e-06 | | |100.00 Nlocal: 416.000 ave 416 max 416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5195.00 ave 5195 max 5195 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: 101864.0 ave 101864 max 101864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 101864 Ave neighs/atom = 244.86538 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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 5 17 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10 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) = 5.017 | 5.017 | 5.017 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 -1372.8591 -1372.8591 20.620033 83.431249 4.0366822 26.255147 26.255147 31.342529 15.669275 31.753636 2.5311944 329.34854 Loop time of 6.886e-06 on 1 procs for 0 steps with 416 atoms 232.4% 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 | | 6.886e-06 | | |100.00 Nlocal: 416.000 ave 416 max 416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5195.00 ave 5195 max 5195 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 50932.0 ave 50932 max 50932 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 101864.0 ave 101864 max 101864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 101864 Ave neighs/atom = 244.86538 Neighbor list builds = 0 Dangerous builds = 0 416 -1372.85911465216 eV 2.53119436383041 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02