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 = 4.0453532 4.0453532 4.0453532 Created orthogonal box = (0.0000000 -43.196598 0.0000000) to (30.541747 43.196598 5.7209934) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.9656616 6.8198768 5.7209934 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -43.196598 0.0000000) to (30.541747 43.196598 5.7209934) create_atoms CPU = 0.001 seconds 458 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.9656616 6.8198768 5.7209934 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -43.196598 0.0000000) to (30.541747 43.196598 5.7209934) 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 10 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 6.25 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 904 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_461927113651_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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 10 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 4.553 | 4.553 | 4.553 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3011.2252 0 -3011.2252 2282.3783 60 0 -3027.4584 0 -3027.4584 -2522.4186 Loop time of 2.60411 on 1 procs for 60 steps with 904 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 = -3011.22515386893 -3027.45579390285 -3027.45837910841 Force two-norm initial, final = 18.878050 0.12070902 Force max component initial, final = 4.6629184 0.011647034 Final line search alpha, max atom move = 1.0000000 0.011647034 Iterations, force evaluations = 60 103 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.5879 | 2.5879 | 2.5879 | 0.0 | 99.38 Neigh | 0.0081183 | 0.0081183 | 0.0081183 | 0.0 | 0.31 Comm | 0.0037219 | 0.0037219 | 0.0037219 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004363 | | | 0.17 Nlocal: 904.000 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3804.00 ave 3804 max 3804 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: 49024.0 ave 49024 max 49024 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 49024 Ave neighs/atom = 54.230088 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 10 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 60 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.553 | 4.553 | 4.553 Mbytes Step Temp E_pair E_mol TotEng Press Volume 60 0 -3027.4584 0 -3027.4584 -2522.4186 15095.408 63 0 -3027.4937 0 -3027.4937 -349.64587 15050.5 Loop time of 0.151683 on 1 procs for 3 steps with 904 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 = -3027.45837910841 -3027.4935057205 -3027.49368978722 Force two-norm initial, final = 32.861398 0.13048302 Force max component initial, final = 25.098920 0.020235295 Final line search alpha, max atom move = 0.00094135858 1.9048669e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.15065 | 0.15065 | 0.15065 | 0.0 | 99.32 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0001736 | 0.0001736 | 0.0001736 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0008569 | | | 0.56 Nlocal: 904.000 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3821.00 ave 3821 max 3821 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: 49048.0 ave 49048 max 49048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 49048 Ave neighs/atom = 54.256637 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 10 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 4.691 | 4.691 | 4.691 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3027.4937 0 -3027.4937 -349.64587 Loop time of 1.581e-06 on 1 procs for 0 steps with 904 atoms 189.8% 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 | | 1.581e-06 | | |100.00 Nlocal: 904.000 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3827.00 ave 3827 max 3827 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: 49072.0 ave 49072 max 49072 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 49072 Ave neighs/atom = 54.283186 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 10 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 4.691 | 4.691 | 4.691 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 -3027.4937 -3027.4937 30.507285 86.393197 5.7104171 -349.64587 -349.64587 -2.1516848 -1045.8772 -0.90874675 2.6678795 763.63659 Loop time of 3.067e-06 on 1 procs for 0 steps with 904 atoms 163.0% 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 | | 3.067e-06 | | |100.00 Nlocal: 904.000 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3827.00 ave 3827 max 3827 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 24536.0 ave 24536 max 24536 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 49072.0 ave 49072 max 49072 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 49072 Ave neighs/atom = 54.283186 Neighbor list builds = 0 Dangerous builds = 0 904 -3027.49368978722 eV 2.66787954974938 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03