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 = 4.0446508 4.0446508 4.0446508 Created orthogonal box = (0.0000000 -59.859410 0.0000000) to (48.871701 59.859410 9.9073306) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0252782 5.7395556 6.6048870 Created 1756 atoms using lattice units in orthogonal box = (0.0000000 -59.859410 0.0000000) to (48.871701 59.859410 9.9073306) create_atoms CPU = 0.002 seconds 1756 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0252782 5.7395556 6.6048870 Created 1756 atoms using lattice units in orthogonal box = (0.0000000 -59.859410 0.0000000) to (48.871701 59.859410 9.9073306) create_atoms CPU = 0.002 seconds 1756 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 16 37 4 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 40 atoms, new total = 3472 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_353977746962_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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 16 37 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.625 | 5.625 | 5.625 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11580.849 0 -11580.849 2043.5192 71 0 -11630.797 0 -11630.797 -3333.1882 Loop time of 22.2329 on 1 procs for 71 steps with 3472 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11580.8485752208 -11630.7867399056 -11630.7973734698 Force two-norm initial, final = 39.886841 0.26621904 Force max component initial, final = 6.7452634 0.027541254 Final line search alpha, max atom move = 1.0000000 0.027541254 Iterations, force evaluations = 71 123 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 22.071 | 22.071 | 22.071 | 0.0 | 99.27 Neigh | 0.10501 | 0.10501 | 0.10501 | 0.0 | 0.47 Comm | 0.021736 | 0.021736 | 0.021736 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03541 | | | 0.16 Nlocal: 3472.00 ave 3472 max 3472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7866.00 ave 7866 max 7866 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: 266128.0 ave 266128 max 266128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 266128 Ave neighs/atom = 76.649770 Neighbor list builds = 3 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 16 37 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 71 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.628 | 5.628 | 5.628 Mbytes Step Temp E_pair E_mol TotEng Press Volume 71 0 -11630.797 0 -11630.797 -3333.1882 57966.428 74 0 -11631.054 0 -11631.054 -159.75085 57730.514 Loop time of 1.03006 on 1 procs for 3 steps with 3472 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 = -11630.7973734699 -11631.048096364 -11631.0544923677 Force two-norm initial, final = 178.06984 9.8105870 Force max component initial, final = 139.50691 9.5872088 Final line search alpha, max atom move = 4.0122040e-05 0.00038465838 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0254 | 1.0254 | 1.0254 | 0.0 | 99.55 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00059397 | 0.00059397 | 0.00059397 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004038 | | | 0.39 Nlocal: 3472.00 ave 3472 max 3472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7845.00 ave 7845 max 7845 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: 266000.0 ave 266000 max 266000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 266000 Ave neighs/atom = 76.612903 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 15 37 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.765 | 5.765 | 5.765 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11631.054 0 -11631.054 -159.75085 Loop time of 6.763e-06 on 1 procs for 0 steps with 3472 atoms 177.4% 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 | | 6.763e-06 | | |100.00 Nlocal: 3472.00 ave 3472 max 3472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7869.00 ave 7869 max 7869 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: 266128.0 ave 266128 max 266128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 266128 Ave neighs/atom = 76.649770 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 15 37 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.765 | 5.765 | 5.765 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 -11631.054 -11631.054 48.75 119.71882 9.8916417 -159.75085 -159.75085 -57.102227 -687.79973 265.64941 2.5593737 1918.7977 Loop time of 4.094e-06 on 1 procs for 0 steps with 3472 atoms 195.4% 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 | | 4.094e-06 | | |100.00 Nlocal: 3472.00 ave 3472 max 3472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7869.00 ave 7869 max 7869 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 133064.0 ave 133064 max 133064 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 266128.0 ave 266128 max 266128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 266128 Ave neighs/atom = 76.649770 Neighbor list builds = 0 Dangerous builds = 0 3472 -11631.0544923677 eV 2.55937369981414 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:24