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 = 3.5620076 3.5620076 3.5620076 Created orthogonal box = (0.0000000 -43.915379 0.0000000) to (15.526431 43.915379 5.0374395) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7202641 4.6226715 5.0374395 Created 304 atoms using lattice units in orthogonal box = (0.0000000 -43.915379 0.0000000) to (15.526431 43.915379 5.0374395) create_atoms CPU = 0.001 seconds 304 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7202641 4.6226715 5.0374395 Created 306 atoms using lattice units in orthogonal box = (0.0000000 -43.915379 0.0000000) to (15.526431 43.915379 5.0374395) create_atoms CPU = 0.001 seconds 306 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 = 7.18 ghost atom cutoff = 7.18 binsize = 3.59, bins = 5 25 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 7.18 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 608 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_763197941039_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 = 7.18 ghost atom cutoff = 7.18 binsize = 3.59, bins = 5 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.18 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) = 4.539 | 4.539 | 4.539 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1813.4266 0 -1813.4266 275688.45 112 0 -2666.3636 0 -2666.3636 10212.417 Loop time of 0.977092 on 1 procs for 112 steps with 608 atoms 96.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1813.42661273398 -2666.36094234483 -2666.36357126334 Force two-norm initial, final = 2073.0114 0.21846248 Force max component initial, final = 464.72689 0.033968026 Final line search alpha, max atom move = 1.0000000 0.033968026 Iterations, force evaluations = 112 214 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.95511 | 0.95511 | 0.95511 | 0.0 | 97.75 Neigh | 0.0055971 | 0.0055971 | 0.0055971 | 0.0 | 0.57 Comm | 0.0092398 | 0.0092398 | 0.0092398 | 0.0 | 0.95 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007146 | | | 0.73 Nlocal: 608.000 ave 608 max 608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4604.00 ave 4604 max 4604 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: 84100.0 ave 84100 max 84100 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 84100 Ave neighs/atom = 138.32237 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 = 7.18 ghost atom cutoff = 7.18 binsize = 3.59, bins = 5 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.18 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 112 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.541 | 4.541 | 4.541 Mbytes Step Temp E_pair E_mol TotEng Press Volume 112 0 -2666.3636 0 -2666.3636 10212.417 6869.5472 124 0 -2666.7675 0 -2666.7675 31.012399 6909.153 Loop time of 0.0615145 on 1 procs for 12 steps with 608 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 = -2666.36357126333 -2666.7649810994 -2666.76749130873 Force two-norm initial, final = 89.405132 1.2561645 Force max component initial, final = 77.611990 0.21598428 Final line search alpha, max atom move = 0.00036196177 7.8178052e-05 Iterations, force evaluations = 12 12 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.053828 | 0.053828 | 0.053828 | 0.0 | 87.50 Neigh | 0.0049561 | 0.0049561 | 0.0049561 | 0.0 | 8.06 Comm | 0.00059535 | 0.00059535 | 0.00059535 | 0.0 | 0.97 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002135 | | | 3.47 Nlocal: 608.000 ave 608 max 608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4872.00 ave 4872 max 4872 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: 84372.0 ave 84372 max 84372 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 84372 Ave neighs/atom = 138.76974 Neighbor list builds = 1 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 = 7.18 ghost atom cutoff = 7.18 binsize = 3.59, bins = 5 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.18 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) = 4.679 | 4.679 | 4.679 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2666.7675 0 -2666.7675 31.012399 Loop time of 1.733e-06 on 1 procs for 0 steps with 608 atoms 173.1% 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 | | 1.733e-06 | | |100.00 Nlocal: 608.000 ave 608 max 608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4872.00 ave 4872 max 4872 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: 84372.0 ave 84372 max 84372 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 84372 Ave neighs/atom = 138.76974 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 = 7.18 ghost atom cutoff = 7.18 binsize = 3.59, bins = 5 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.18 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) = 4.679 | 4.679 | 4.679 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 -2666.7675 -2666.7675 15.519842 88.884727 5.008531 31.012399 31.012399 50.063746 -4.7440076 47.71746 2.3829719 376.02147 Loop time of 2.172e-06 on 1 procs for 0 steps with 608 atoms 184.2% 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 | | 2.172e-06 | | |100.00 Nlocal: 608.000 ave 608 max 608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4872.00 ave 4872 max 4872 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 42186.0 ave 42186 max 42186 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 84372.0 ave 84372 max 84372 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 84372 Ave neighs/atom = 138.76974 Neighbor list builds = 0 Dangerous builds = 0 608 -2666.76749130873 eV 2.38297186842967 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01