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 = 3.6580991 3.6580991 3.6580991 Created orthogonal box = (0.0000000 -54.138582 0.0000000) to (44.200980 54.138582 8.9604763) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4494359 5.1910201 5.9736509 Created 1758 atoms using lattice units in orthogonal box = (0.0000000 -54.138582 0.0000000) to (44.200980 54.138582 8.9604763) create_atoms CPU = 0.002 seconds 1758 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4494359 5.1910201 5.9736509 Created 1758 atoms using lattice units in orthogonal box = (0.0000000 -54.138582 0.0000000) to (44.200980 54.138582 8.9604763) create_atoms CPU = 0.002 seconds 1758 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 13 30 3 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 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 44 atoms, new total = 3472 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_634187028437_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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 13 30 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 6.562 | 6.562 | 6.562 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13414.281 0 -13414.281 526.13272 888 0 -13622.534 0 -13622.534 -51347.818 Loop time of 37.2861 on 1 procs for 888 steps with 3472 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 = -13414.2805357445 -13622.5218418371 -13622.5341454983 Force two-norm initial, final = 46.613339 0.34730127 Force max component initial, final = 7.5841802 0.032591367 Final line search alpha, max atom move = 1.0000000 0.032591367 Iterations, force evaluations = 888 1727 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 36.497 | 36.497 | 36.497 | 0.0 | 97.88 Neigh | 0.41467 | 0.41467 | 0.41467 | 0.0 | 1.11 Comm | 0.15819 | 0.15819 | 0.15819 | 0.0 | 0.42 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.2164 | | | 0.58 Nlocal: 3472.00 ave 3472 max 3472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10331.0 ave 10331 max 10331 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: 476134.0 ave 476134 max 476134 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 476134 Ave neighs/atom = 137.13537 Neighbor list builds = 14 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 13 30 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 888 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.564 | 6.564 | 6.564 Mbytes Step Temp E_pair E_mol TotEng Press Volume 888 0 -13622.534 0 -13622.534 -51347.818 42884.452 922 0 -13649.27 0 -13649.27 -21363.653 41978.203 Loop time of 0.777533 on 1 procs for 34 steps with 3472 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 = -13622.534145498 -13649.2665721405 -13649.270447429 Force two-norm initial, final = 1665.0101 4.8862611 Force max component initial, final = 1657.0616 1.0595563 Final line search alpha, max atom move = 9.1332577e-05 9.6772003e-05 Iterations, force evaluations = 34 35 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.72596 | 0.72596 | 0.72596 | 0.0 | 93.37 Neigh | 0.029971 | 0.029971 | 0.029971 | 0.0 | 3.85 Comm | 0.0029723 | 0.0029723 | 0.0029723 | 0.0 | 0.38 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01863 | | | 2.40 Nlocal: 3472.00 ave 3472 max 3472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10339.0 ave 10339 max 10339 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: 483124.0 ave 483124 max 483124 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 483124 Ave neighs/atom = 139.14862 Neighbor list builds = 1 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 12 30 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 6.701 | 6.701 | 6.701 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13649.27 0 -13649.27 -21363.653 Loop time of 1.522e-06 on 1 procs for 0 steps with 3472 atoms 197.1% 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 | | 1.522e-06 | | |100.00 Nlocal: 3472.00 ave 3472 max 3472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10299.0 ave 10299 max 10299 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: 483916.0 ave 483916 max 483916 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 483916 Ave neighs/atom = 139.37673 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 12 30 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 6.701 | 6.701 | 6.701 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 -13649.27 -13649.27 42.745846 108.27716 9.0697027 -21363.653 -21363.653 38.853239 -64088.881 -40.932898 2.3055983 5340.8915 Loop time of 1.899e-06 on 1 procs for 0 steps with 3472 atoms 210.6% 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 | | 1.899e-06 | | |100.00 Nlocal: 3472.00 ave 3472 max 3472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10299.0 ave 10299 max 10299 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 241958.0 ave 241958 max 241958 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 483916.0 ave 483916 max 483916 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 483916 Ave neighs/atom = 139.37673 Neighbor list builds = 0 Dangerous builds = 0 3472 -13158.2545692022 eV 2.30559832775763 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:38