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 = 4.0452705 4.0452705 4.0452705 Created orthogonal box = (0.0000000 -77.390581 0.0000000) to (44.681473 77.390581 7.0066140) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.5923484 5.9205909 7.0066140 Created 1463 atoms using lattice units in orthogonal box = (0.0000000 -77.390581 0.0000000) to (44.681473 77.390581 7.0066140) create_atoms CPU = 0.003 seconds 1463 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.5923484 5.9205909 7.0066140 Created 1465 atoms using lattice units in orthogonal box = (0.0000000 -77.390581 0.0000000) to (44.681473 77.390581 7.0066140) create_atoms CPU = 0.003 seconds 1465 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 = 9.5 ghost atom cutoff = 9.5 binsize = 4.75, bins = 10 33 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 9.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 2924 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_658278549784_005#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 = 9.5 ghost atom cutoff = 9.5 binsize = 4.75, bins = 10 33 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.5 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) = 11.31 | 11.31 | 11.31 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9807.1184 0 -9807.1184 10087.993 70 0 -9949.0078 0 -9949.0078 2991.4112 Loop time of 3.817 on 1 procs for 70 steps with 2924 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 = -9807.11843589956 -9949.00027067359 -9949.00779079792 Force two-norm initial, final = 176.62947 0.17913667 Force max component initial, final = 65.036854 0.025894809 Final line search alpha, max atom move = 1.0000000 0.025894809 Iterations, force evaluations = 70 125 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.6706 | 3.6706 | 3.6706 | 0.0 | 96.16 Neigh | 0.10954 | 0.10954 | 0.10954 | 0.0 | 2.87 Comm | 0.020349 | 0.020349 | 0.020349 | 0.0 | 0.53 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01653 | | | 0.43 Nlocal: 2924.00 ave 2924 max 2924 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15571.0 ave 15571 max 15571 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: 644546.0 ave 644546 max 644546 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 644546 Ave neighs/atom = 220.43297 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 = 9.5 ghost atom cutoff = 9.5 binsize = 4.75, bins = 10 33 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 70 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 11.31 | 11.31 | 11.31 Mbytes Step Temp E_pair E_mol TotEng Press Volume 70 0 -9949.0078 0 -9949.0078 2991.4112 48456.693 75 0 -9949.3032 0 -9949.3032 -3.9174584 48637.781 Loop time of 0.238129 on 1 procs for 5 steps with 2924 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 = -9949.00779079794 -9949.30000200603 -9949.30318852422 Force two-norm initial, final = 171.94811 0.83078123 Force max component initial, final = 148.20805 0.65634260 Final line search alpha, max atom move = 4.4723144e-05 2.9353704e-05 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.23294 | 0.23294 | 0.23294 | 0.0 | 97.82 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00091162 | 0.00091162 | 0.00091162 | 0.0 | 0.38 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004283 | | | 1.80 Nlocal: 2924.00 ave 2924 max 2924 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15553.0 ave 15553 max 15553 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: 644724.0 ave 644724 max 644724 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 644724 Ave neighs/atom = 220.49384 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 = 9.5 ghost atom cutoff = 9.5 binsize = 4.75, bins = 10 33 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.5 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) = 10.83 | 10.83 | 10.83 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9949.3032 0 -9949.3032 -3.9174584 Loop time of 1.718e-06 on 1 procs for 0 steps with 2924 atoms 116.4% 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 | | 1.718e-06 | | |100.00 Nlocal: 2924.00 ave 2924 max 2924 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15558.0 ave 15558 max 15558 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: 638634.0 ave 638634 max 638634 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 638634 Ave neighs/atom = 218.41108 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 = 9.5 ghost atom cutoff = 9.5 binsize = 4.75, bins = 10 33 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.5 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) = 10.83 | 10.83 | 10.83 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 -9949.3032 -9949.3032 44.662129 155.43751 7.0061349 -3.9174584 -3.9174584 -21.611213 -4.4658476 14.324685 2.4312229 1229.8684 Loop time of 2.349e-06 on 1 procs for 0 steps with 2924 atoms 212.9% 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 | | 2.349e-06 | | |100.00 Nlocal: 2924.00 ave 2924 max 2924 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15558.0 ave 15558 max 15558 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 319317.0 ave 319317 max 319317 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 638634.0 ave 638634 max 638634 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 638634 Ave neighs/atom = 218.41108 Neighbor list builds = 0 Dangerous builds = 0 2924 -9949.30318852422 eV 2.43122290606342 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04