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 = 3.6584036 3.6584036 3.6584036 Created orthogonal box = (0.0000000 -69.989382 0.0000000) to (40.408388 69.989382 6.3365409) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9618934 5.3543789 6.3365409 Created 1464 atoms using lattice units in orthogonal box = (0.0000000 -69.989382 0.0000000) to (40.408388 69.989382 6.3365409) create_atoms CPU = 0.003 seconds 1464 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9618934 5.3543789 6.3365409 Created 1466 atoms using lattice units in orthogonal box = (0.0000000 -69.989382 0.0000000) to (40.408388 69.989382 6.3365409) create_atoms CPU = 0.003 seconds 1466 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 = 12 39 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 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 2930 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_143977152728_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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 12 39 2 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) = 6.593 | 6.593 | 6.593 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10839.598 0 -10839.598 53520.309 808 0 -11572.236 0 -11572.236 -63569.886 Loop time of 34.525 on 1 procs for 808 steps with 2930 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 = -10839.5979603418 -11572.2245784809 -11572.2358608496 Force two-norm initial, final = 825.36311 0.41002965 Force max component initial, final = 208.52208 0.14972208 Final line search alpha, max atom move = 0.86244106 0.12912647 Iterations, force evaluations = 808 1577 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 33.629 | 33.629 | 33.629 | 0.0 | 97.40 Neigh | 0.41219 | 0.41219 | 0.41219 | 0.0 | 1.19 Comm | 0.24533 | 0.24533 | 0.24533 | 0.0 | 0.71 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.2388 | | | 0.69 Nlocal: 2930.00 ave 2930 max 2930 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11614.0 ave 11614 max 11614 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: 397486.0 ave 397486 max 397486 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 397486 Ave neighs/atom = 135.66075 Neighbor list builds = 16 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 = 12 39 2 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 : 808 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.592 | 6.592 | 6.592 Mbytes Step Temp E_pair E_mol TotEng Press Volume 808 0 -11572.236 0 -11572.236 -63569.886 35841.479 835 0 -11609.869 0 -11609.869 -3.755588 34325.136 Loop time of 0.716956 on 1 procs for 27 steps with 2930 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 = -11572.2358608497 -11609.8657324063 -11609.8693147358 Force two-norm initial, final = 2539.0947 5.3323222 Force max component initial, final = 1738.5082 1.5699131 Final line search alpha, max atom move = 9.1287994e-05 0.00014331422 Iterations, force evaluations = 27 28 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.615 | 0.615 | 0.615 | 0.0 | 85.78 Neigh | 0.080307 | 0.080307 | 0.080307 | 0.0 | 11.20 Comm | 0.0037221 | 0.0037221 | 0.0037221 | 0.0 | 0.52 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01793 | | | 2.50 Nlocal: 2930.00 ave 2930 max 2930 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11698.0 ave 11698 max 11698 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: 413518.0 ave 413518 max 413518 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 413518 Ave neighs/atom = 141.13242 Neighbor list builds = 3 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 = 11 38 2 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) = 6.729 | 6.729 | 6.729 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11609.869 0 -11609.869 -3.755588 Loop time of 2.239e-06 on 1 procs for 0 steps with 2930 atoms 178.7% 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 | | 2.239e-06 | | |100.00 Nlocal: 2930.00 ave 2930 max 2930 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11688.0 ave 11688 max 11688 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: 412968.0 ave 412968 max 412968 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 412968 Ave neighs/atom = 140.94471 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 = 11 38 2 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) = 6.729 | 6.729 | 6.729 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 -11609.869 -11609.869 39.59792 136.51384 6.3498462 -3.755588 -3.755588 19.11914 43.045978 -73.431881 2.1880588 9669.2518 Loop time of 2.284e-06 on 1 procs for 0 steps with 2930 atoms 262.7% 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 | | 2.284e-06 | | |100.00 Nlocal: 2930.00 ave 2930 max 2930 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11688.0 ave 11688 max 11688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 206484.0 ave 206484 max 206484 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 412968.0 ave 412968 max 412968 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 412968 Ave neighs/atom = 140.94471 Neighbor list builds = 0 Dangerous builds = 0 2930 -11609.8693147358 eV 2.18805880006386 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:36