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 = 2.8553125 2.8553125 2.8553125 Created orthogonal box = (0.0000000 -34.500873 0.0000000) to (42.254767 34.500873 6.9940587) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.0518269 4.2535322 4.6627058 Created 872 atoms using lattice units in orthogonal box = (0.0000000 -34.500873 0.0000000) to (42.254767 34.500873 6.9940587) create_atoms CPU = 0.003 seconds 872 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.0518269 4.2535322 4.6627058 Created 878 atoms using lattice units in orthogonal box = (0.0000000 -34.500873 0.0000000) to (42.254767 34.500873 6.9940587) create_atoms CPU = 0.003 seconds 878 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 12 19 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 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 1742 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_143977152728_005#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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 12 19 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.546 | 5.546 | 5.546 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3743.1454 0 -3743.1454 352326.5 104 0 -6946.2779 0 -6946.2779 760.81656 Loop time of 5.03065 on 1 procs for 104 steps with 1742 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 = -3743.14539238897 -6946.27258125208 -6946.27785194591 Force two-norm initial, final = 5180.6624 0.25099492 Force max component initial, final = 889.58015 0.086009807 Final line search alpha, max atom move = 0.63573193 0.054679181 Iterations, force evaluations = 104 189 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.8948 | 4.8948 | 4.8948 | 0.0 | 97.30 Neigh | 0.070117 | 0.070117 | 0.070117 | 0.0 | 1.39 Comm | 0.029394 | 0.029394 | 0.029394 | 0.0 | 0.58 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0363 | | | 0.72 Nlocal: 1742.00 ave 1742 max 1742 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6754.00 ave 6754 max 6754 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: 237234.0 ave 237234 max 237234 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 237234 Ave neighs/atom = 136.18485 Neighbor list builds = 2 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 12 19 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 104 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.547 | 5.547 | 5.547 Mbytes Step Temp E_pair E_mol TotEng Press Volume 104 0 -6946.2779 0 -6946.2779 760.81656 20392.246 108 0 -6946.4296 0 -6946.4296 -72.294451 20403.264 Loop time of 0.158521 on 1 procs for 4 steps with 1742 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 = -6946.2778519459 -6946.42805013341 -6946.42961652742 Force two-norm initial, final = 76.700509 1.6624522 Force max component initial, final = 69.274947 0.99756606 Final line search alpha, max atom move = 0.00016118994 0.00016079761 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.15413 | 0.15413 | 0.15413 | 0.0 | 97.23 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00090687 | 0.00090687 | 0.00090687 | 0.0 | 0.57 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003482 | | | 2.20 Nlocal: 1742.00 ave 1742 max 1742 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6754.00 ave 6754 max 6754 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: 236774.0 ave 236774 max 236774 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 236774 Ave neighs/atom = 135.92078 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 12 19 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.685 | 5.685 | 5.685 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6946.4296 0 -6946.4296 -72.294451 Loop time of 6.315e-06 on 1 procs for 0 steps with 1742 atoms 174.2% 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 | | 6.315e-06 | | |100.00 Nlocal: 1742.00 ave 1742 max 1742 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6760.00 ave 6760 max 6760 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: 236634.0 ave 236634 max 236634 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 236634 Ave neighs/atom = 135.84041 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 12 19 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.685 | 5.685 | 5.685 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 -6946.4296 -6946.4296 42.164917 69.231446 6.9894819 -72.294451 -72.294451 -78.167807 -64.734282 -73.981264 2.239107 1563.9679 Loop time of 6.896e-06 on 1 procs for 0 steps with 1742 atoms 246.5% 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 | | 6.896e-06 | | |100.00 Nlocal: 1742.00 ave 1742 max 1742 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6760.00 ave 6760 max 6760 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 118317.0 ave 118317 max 118317 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 236634.0 ave 236634 max 236634 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 236634 Ave neighs/atom = 135.84041 Neighbor list builds = 0 Dangerous builds = 0 1742 -6946.42961652742 eV 2.23910704536261 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06