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 = 3.4986965 3.4986965 3.4986965 Created orthogonal box = (0.0000000 -51.423626 0.0000000) to (18.179760 51.423626 4.9479041) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.7132712 5.7133475 4.9479041 Created 434 atoms using lattice units in orthogonal box = (0.0000000 -51.423626 0.0000000) to (18.179760 51.423626 4.9479041) create_atoms CPU = 0.001 seconds 434 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.7132712 5.7133475 4.9479041 Created 434 atoms using lattice units in orthogonal box = (0.0000000 -51.423626 0.0000000) to (18.179760 51.423626 4.9479041) 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 5 28 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 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 856 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_677715648236_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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 5 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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 -3440.146 0 -3440.146 46743.564 48 0 -3510.467 0 -3510.467 -5846.2967 Loop time of 0.648977 on 1 procs for 48 steps with 856 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 = -3440.14599642249 -3510.46352762685 -3510.46703145149 Force two-norm initial, final = 172.33887 0.25595198 Force max component initial, final = 62.703307 0.042062926 Final line search alpha, max atom move = 1.0000000 0.042062926 Iterations, force evaluations = 48 85 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.63231 | 0.63231 | 0.63231 | 0.0 | 97.43 Neigh | 0.0088888 | 0.0088888 | 0.0088888 | 0.0 | 1.37 Comm | 0.0044835 | 0.0044835 | 0.0044835 | 0.0 | 0.69 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003291 | | | 0.51 Nlocal: 856.000 ave 856 max 856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6845.00 ave 6845 max 6845 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: 149292.0 ave 149292 max 149292 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 149292 Ave neighs/atom = 174.40654 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 5 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 48 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.014 | 5.014 | 5.014 Mbytes Step Temp E_pair E_mol TotEng Press Volume 48 0 -3510.467 0 -3510.467 -5846.2967 9251.2863 54 0 -3510.5648 0 -3510.5648 -1941.4979 9219.2504 Loop time of 0.0620683 on 1 procs for 6 steps with 856 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 = -3510.4670314515 -3510.56471655638 -3510.56475134628 Force two-norm initial, final = 41.084901 0.48885422 Force max component initial, final = 40.742934 0.29651060 Final line search alpha, max atom move = 0.0013752738 0.00040778326 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.060023 | 0.060023 | 0.060023 | 0.0 | 96.70 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00039541 | 0.00039541 | 0.00039541 | 0.0 | 0.64 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00165 | | | 2.66 Nlocal: 856.000 ave 856 max 856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6846.00 ave 6846 max 6846 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: 149220.0 ave 149220 max 149220 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 149220 Ave neighs/atom = 174.32243 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 5 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 5.152 | 5.152 | 5.152 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3510.5648 0 -3510.5648 -1941.4979 Loop time of 1.539e-06 on 1 procs for 0 steps with 856 atoms 194.9% 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 | | 1.539e-06 | | |100.00 Nlocal: 856.000 ave 856 max 856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6854.00 ave 6854 max 6854 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: 149256.0 ave 149256 max 149256 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 149256 Ave neighs/atom = 174.36449 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 5 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 5.152 | 5.152 | 5.152 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 -3510.5648 -3510.5648 18.087875 102.84725 4.9558182 -1941.4979 -1941.4979 -0.71189378 -5875.3937 51.611807 2.2511734 451.95496 Loop time of 1.0595e-05 on 1 procs for 0 steps with 856 atoms 122.7% 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 | | 1.06e-05 | | |100.00 Nlocal: 856.000 ave 856 max 856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6854.00 ave 6854 max 6854 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 74628.0 ave 74628 max 74628 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 149256.0 ave 149256 max 149256 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 149256 Ave neighs/atom = 174.36449 Neighbor list builds = 0 Dangerous builds = 0 856 -3510.56475134628 eV 2.25117342667558 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01