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 = 3.6330168 3.6330168 3.6330168 Created orthogonal box = (0.0000000 -42.371525 0.0000000) to (14.979312 42.371525 5.1378616) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.1679520 6.2305724 5.1378616 Created 274 atoms using lattice units in orthogonal box = (0.0000000 -42.371525 0.0000000) to (14.979312 42.371525 5.1378616) create_atoms CPU = 0.001 seconds 274 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.1679520 6.2305724 5.1378616 Created 274 atoms using lattice units in orthogonal box = (0.0000000 -42.371525 0.0000000) to (14.979312 42.371525 5.1378616) create_atoms CPU = 0.001 seconds 274 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 4 22 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 7.709524 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 540 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_036303866285_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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 4 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 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) = 4.531 | 4.531 | 4.531 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2271.8513 0 -2271.8513 16327.733 67 0 -2300.5222 0 -2300.5222 -5542.6519 Loop time of 0.525641 on 1 procs for 67 steps with 540 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 = -2271.85134958156 -2300.51995211718 -2300.52223234163 Force two-norm initial, final = 51.325880 0.19403525 Force max component initial, final = 20.048146 0.037646097 Final line search alpha, max atom move = 1.0000000 0.037646097 Iterations, force evaluations = 67 122 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.50952 | 0.50952 | 0.50952 | 0.0 | 96.93 Neigh | 0.0064652 | 0.0064652 | 0.0064652 | 0.0 | 1.23 Comm | 0.0057773 | 0.0057773 | 0.0057773 | 0.0 | 1.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003879 | | | 0.74 Nlocal: 540.000 ave 540 max 540 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4959.00 ave 4959 max 4959 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: 86724.0 ave 86724 max 86724 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 86724 Ave neighs/atom = 160.60000 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 4 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 67 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.531 | 4.531 | 4.531 Mbytes Step Temp E_pair E_mol TotEng Press Volume 67 0 -2300.5222 0 -2300.5222 -5542.6519 6521.9634 69 0 -2300.5268 0 -2300.5268 -3994.9645 6515.2001 Loop time of 0.0217578 on 1 procs for 2 steps with 540 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 = -2300.52223234163 -2300.52680769425 -2300.52684805276 Force two-norm initial, final = 11.910672 0.20325277 Force max component initial, final = 10.065159 0.050433646 Final line search alpha, max atom move = 0.0015140754 7.6360341e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.020714 | 0.020714 | 0.020714 | 0.0 | 95.20 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00020817 | 0.00020817 | 0.00020817 | 0.0 | 0.96 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0008357 | | | 3.84 Nlocal: 540.000 ave 540 max 540 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4951.00 ave 4951 max 4951 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: 82920.0 ave 82920 max 82920 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 82920 Ave neighs/atom = 153.55556 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 4 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 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) = 4.669 | 4.669 | 4.669 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2300.5268 0 -2300.5268 -3994.9645 Loop time of 1.939e-06 on 1 procs for 0 steps with 540 atoms 154.7% 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 | | 1.939e-06 | | |100.00 Nlocal: 540.000 ave 540 max 540 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4951.00 ave 4951 max 4951 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: 84624.0 ave 84624 max 84624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 84624 Ave neighs/atom = 156.71111 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 4 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 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) = 4.669 | 4.669 | 4.669 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 -2300.5268 -2300.5268 14.968778 84.74305 5.1361454 -3994.9645 -3994.9645 3.8102363 -11976.306 -12.398178 2.4027257 301.11686 Loop time of 2.721e-06 on 1 procs for 0 steps with 540 atoms 183.8% 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 | | 2.721e-06 | | |100.00 Nlocal: 540.000 ave 540 max 540 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4951.00 ave 4951 max 4951 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 42312.0 ave 42312 max 42312 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 84624.0 ave 84624 max 84624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 84624 Ave neighs/atom = 156.71111 Neighbor list builds = 0 Dangerous builds = 0 540 -2300.52684805276 eV 2.40272568902344 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01