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 = 3.5200000 3.5200000 3.5200000 Created orthogonal box = (0.0000000 -67.345086 0.0000000) to (38.879671 67.345086 6.0968189) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7363449 5.1518138 6.0968189 Created 1466 atoms using lattice units in orthogonal box = (0.0000000 -67.345086 0.0000000) to (38.879671 67.345086 6.0968189) create_atoms CPU = 0.002 seconds 1466 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7363449 5.1518138 6.0968189 Created 1466 atoms using lattice units in orthogonal box = (0.0000000 -67.345086 0.0000000) to (38.879671 67.345086 6.0968189) create_atoms CPU = 0.002 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 10 32 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 28 atoms, new total = 2904 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_103383163946_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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 10 32 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 11.32 | 11.32 | 11.32 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12845.831 0 -12845.831 2413.4015 42 0 -12882.744 0 -12882.744 -8423.1393 Loop time of 2.28624 on 1 procs for 42 steps with 2904 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 = -12845.8306434234 -12882.7323537208 -12882.7439544054 Force two-norm initial, final = 54.153814 0.33566511 Force max component initial, final = 9.4210641 0.044828987 Final line search alpha, max atom move = 0.87084089 0.039038915 Iterations, force evaluations = 42 77 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.2266 | 2.2266 | 2.2266 | 0.0 | 97.39 Neigh | 0.037215 | 0.037215 | 0.037215 | 0.0 | 1.63 Comm | 0.012225 | 0.012225 | 0.012225 | 0.0 | 0.53 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01015 | | | 0.44 Nlocal: 2904.00 ave 2904 max 2904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15840.0 ave 15840 max 15840 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: 649852.0 ave 649852 max 649852 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 649852 Ave neighs/atom = 223.77824 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 10 32 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 42 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 11.32 | 11.32 | 11.32 Mbytes Step Temp E_pair E_mol TotEng Press Volume 42 0 -12882.744 0 -12882.744 -8423.1393 31927.27 45 0 -12882.901 0 -12882.901 -3755.9398 31843.009 Loop time of 0.175902 on 1 procs for 3 steps with 2904 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 = -12882.7439544054 -12882.8993241598 -12882.900640696 Force two-norm initial, final = 158.59198 0.35039549 Force max component initial, final = 130.94601 0.049861911 Final line search alpha, max atom move = 0.00010229586 5.1006670e-06 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.17218 | 0.17218 | 0.17218 | 0.0 | 97.88 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00068972 | 0.00068972 | 0.00068972 | 0.0 | 0.39 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003035 | | | 1.73 Nlocal: 2904.00 ave 2904 max 2904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15840.0 ave 15840 max 15840 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: 649860.0 ave 649860 max 649860 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 649860 Ave neighs/atom = 223.78099 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 10 32 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 10.83 | 10.83 | 10.83 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12882.901 0 -12882.901 -3755.9398 Loop time of 1.59e-06 on 1 procs for 0 steps with 2904 atoms 188.7% 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 | | 1.59e-06 | | |100.00 Nlocal: 2904.00 ave 2904 max 2904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15872.0 ave 15872 max 15872 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: 649980.0 ave 649980 max 649980 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 649980 Ave neighs/atom = 223.82231 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 10 32 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 10.83 | 10.83 | 10.83 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 -12882.901 -12882.901 38.808095 134.69017 6.0919435 -3755.9398 -3755.9398 -1.449749 -11263.863 -2.5067888 2.2287069 856.71646 Loop time of 3.652e-06 on 1 procs for 0 steps with 2904 atoms 191.7% 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 | | 3.652e-06 | | |100.00 Nlocal: 2904.00 ave 2904 max 2904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15872.0 ave 15872 max 15872 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 324990.0 ave 324990 max 324990 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 649980.0 ave 649980 max 649980 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 649980 Ave neighs/atom = 223.82231 Neighbor list builds = 0 Dangerous builds = 0 2904 -12803.8208978704 eV 2.22870693884746 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03