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 = 3.5200008 3.5200008 3.5200008 Created orthogonal box = (0.0000000 -51.736755 0.0000000) to (18.290461 51.736755 4.9780328) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.7419712 5.7481372 4.9780328 Created 434 atoms using lattice units in orthogonal box = (0.0000000 -51.736755 0.0000000) to (18.290461 51.736755 4.9780328) create_atoms CPU = 0.002 seconds 434 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.7419712 5.7481372 4.9780328 Created 434 atoms using lattice units in orthogonal box = (0.0000000 -51.736755 0.0000000) to (18.290461 51.736755 4.9780328) create_atoms CPU = 0.001 seconds 434 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 5 27 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 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 10 atoms, new total = 858 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_657255834688_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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 5 27 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 5.014 | 5.014 | 5.014 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3776.1584 0 -3776.1584 3266.4245 44 0 -3800.9857 0 -3800.9857 -2934.2001 Loop time of 0.694563 on 1 procs for 44 steps with 858 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 = -3776.15838263597 -3800.98212116913 -3800.98566090986 Force two-norm initial, final = 30.758380 0.23845234 Force max component initial, final = 9.4141334 0.063681665 Final line search alpha, max atom move = 1.0000000 0.063681665 Iterations, force evaluations = 44 83 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.67496 | 0.67496 | 0.67496 | 0.0 | 97.18 Neigh | 0.010103 | 0.010103 | 0.010103 | 0.0 | 1.45 Comm | 0.0056 | 0.0056 | 0.0056 | 0.0 | 0.81 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003901 | | | 0.56 Nlocal: 858.000 ave 858 max 858 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6905.00 ave 6905 max 6905 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: 150968.0 ave 150968 max 150968 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 150968 Ave neighs/atom = 175.95338 Neighbor list builds = 1 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 5 27 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 44 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.016 | 5.016 | 5.016 Mbytes Step Temp E_pair E_mol TotEng Press Volume 44 0 -3800.9857 0 -3800.9857 -2934.2001 9421.3161 46 0 -3801.0081 0 -3801.0081 463.43148 9403.9813 Loop time of 0.0421937 on 1 procs for 2 steps with 858 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 = -3800.98566090986 -3801.00729726393 -3801.00810186636 Force two-norm initial, final = 33.384442 0.24604151 Force max component initial, final = 25.552685 0.059541805 Final line search alpha, max atom move = 0.00035902058 2.1376733e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.040743 | 0.040743 | 0.040743 | 0.0 | 96.56 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00028013 | 0.00028013 | 0.00028013 | 0.0 | 0.66 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00117 | | | 2.77 Nlocal: 858.000 ave 858 max 858 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6905.00 ave 6905 max 6905 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: 150916.0 ave 150916 max 150916 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 150916 Ave neighs/atom = 175.89277 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 5 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 5.154 | 5.154 | 5.154 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3801.0081 0 -3801.0081 463.43148 Loop time of 1.913e-06 on 1 procs for 0 steps with 858 atoms 156.8% 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 | | 1.913e-06 | | |100.00 Nlocal: 858.000 ave 858 max 858 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6921.00 ave 6921 max 6921 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: 151012.0 ave 151012 max 151012 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 151012 Ave neighs/atom = 176.00466 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 5 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 5.154 | 5.154 | 5.154 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 -3801.0081 -3801.0081 18.266648 103.47351 4.9753509 463.43148 463.43148 2.668308 1397.7649 -10.1388 2.270381 436.96554 Loop time of 1.0018e-05 on 1 procs for 0 steps with 858 atoms 139.7% 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 | | 1.002e-05 | | |100.00 Nlocal: 858.000 ave 858 max 858 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6921.00 ave 6921 max 6921 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 75506.0 ave 75506 max 75506 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 151012.0 ave 151012 max 151012 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 151012 Ave neighs/atom = 176.00466 Neighbor list builds = 0 Dangerous builds = 0 858 -3801.00810186636 eV 2.27038104522695 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01