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 = 3.1674131 3.1674131 3.1674131 Created orthogonal box = (0.0000000 -47.826889 0.0000000) to (33.818718 47.826889 4.4793986) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3397975 4.6148753 4.4793986 Created 456 atoms using lattice units in orthogonal box = (0.0000000 -47.826889 0.0000000) to (33.818718 47.826889 4.4793986) create_atoms CPU = 0.002 seconds 456 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.3397975 4.6148753 4.4793986 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -47.826889 0.0000000) to (33.818718 47.826889 4.4793986) create_atoms CPU = 0.001 seconds 458 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 = 7.9 ghost atom cutoff = 7.9 binsize = 3.95, bins = 9 25 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 7.9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 908 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_269937397263_001#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 = 7.9 ghost atom cutoff = 7.9 binsize = 3.95, bins = 9 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.9 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) = 4.972 | 4.972 | 4.972 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6019.3882 0 -6019.3882 3933.7964 70 0 -6152.2134 0 -6152.2134 339.51168 Loop time of 9.69575 on 1 procs for 70 steps with 908 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 = -6019.38822409963 -6152.20892471252 -6152.21342046962 Force two-norm initial, final = 51.708787 0.20434097 Force max component initial, final = 10.158357 0.016483775 Final line search alpha, max atom move = 1.0000000 0.016483775 Iterations, force evaluations = 70 102 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 9.6564 | 9.6564 | 9.6564 | 0.0 | 99.59 Neigh | 0.026433 | 0.026433 | 0.026433 | 0.0 | 0.27 Comm | 0.0067852 | 0.0067852 | 0.0067852 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006097 | | | 0.06 Nlocal: 908.000 ave 908 max 908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6501.00 ave 6501 max 6501 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: 122060.0 ave 122060 max 122060 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 122060 Ave neighs/atom = 134.42731 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 = 7.9 ghost atom cutoff = 7.9 binsize = 3.95, bins = 9 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.9 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) = 4.983 | 4.983 | 4.983 Mbytes Step Temp E_pair E_mol TotEng Press Volume 70 0 -6152.2134 0 -6152.2134 339.51168 14490.353 73 0 -6152.2649 0 -6152.2649 -2.4658142 14492.418 Loop time of 0.551647 on 1 procs for 3 steps with 908 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -6152.21342046961 -6152.26460930568 -6152.26491894102 Force two-norm initial, final = 47.111939 0.26858097 Force max component initial, final = 40.543114 0.083134340 Final line search alpha, max atom move = 0.00018441006 1.5330808e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.54994 | 0.54994 | 0.54994 | 0.0 | 99.69 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00030991 | 0.00030991 | 0.00030991 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001394 | | | 0.25 Nlocal: 908.000 ave 908 max 908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6827.00 ave 6827 max 6827 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: 122068.0 ave 122068 max 122068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 122068 Ave neighs/atom = 134.43612 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 = 7.9 ghost atom cutoff = 7.9 binsize = 3.95, bins = 9 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.9 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) = 5.121 | 5.121 | 5.121 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6152.2649 0 -6152.2649 -2.4658142 Loop time of 2.171e-06 on 1 procs for 0 steps with 908 atoms 184.2% 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 | | 2.171e-06 | | |100.00 Nlocal: 908.000 ave 908 max 908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6827.00 ave 6827 max 6827 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: 122016.0 ave 122016 max 122016 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 122016 Ave neighs/atom = 134.37885 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 = 7.9 ghost atom cutoff = 7.9 binsize = 3.95, bins = 9 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.9 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) = 5.121 | 5.121 | 5.121 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 -6152.2649 -6152.2649 33.801194 95.826227 4.4742929 -2.4658142 -2.4658142 6.4880334 -4.7052226 -9.1802533 2.5025594 709.98948 Loop time of 2.269e-06 on 1 procs for 0 steps with 908 atoms 132.2% 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 | | 2.269e-06 | | |100.00 Nlocal: 908.000 ave 908 max 908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6827.00 ave 6827 max 6827 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 61008.0 ave 61008 max 61008 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 122016.0 ave 122016 max 122016 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 122016 Ave neighs/atom = 134.37885 Neighbor list builds = 0 Dangerous builds = 0 908 -6152.26491894102 eV 2.50255939328577 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:10