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 = 3.6073527 3.6073527 3.6073527 Created orthogonal box = (0.0000000 -39.516569 0.0000000) to (8.0662859 39.516569 8.8361734) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8397715 5.2688759 5.8907823 Created 240 atoms using lattice units in orthogonal box = (0.0000000 -39.516569 0.0000000) to (8.0662859 39.516569 8.8361734) create_atoms CPU = 0.001 seconds 240 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8397715 5.2688759 5.8907823 Created 242 atoms using lattice units in orthogonal box = (0.0000000 -39.516569 0.0000000) to (8.0662859 39.516569 8.8361734) create_atoms CPU = 0.000 seconds 242 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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 2 14 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 12.1544 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 476 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_151002396060_004#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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 2 14 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.1544 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) = 5.899 | 5.899 | 5.899 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1596.9068 0 -1596.9068 22308.874 83 0 -1669.2689 0 -1669.2689 -4086.6577 Loop time of 2.06875 on 1 procs for 83 steps with 476 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 = -1596.90681462683 -1669.26755301132 -1669.26890134517 Force two-norm initial, final = 149.15362 0.13470377 Force max component initial, final = 52.367997 0.013150503 Final line search alpha, max atom move = 1.0000000 0.013150503 Iterations, force evaluations = 83 153 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.021 | 2.021 | 2.021 | 0.0 | 97.69 Neigh | 0.029552 | 0.029552 | 0.029552 | 0.0 | 1.43 Comm | 0.012547 | 0.012547 | 0.012547 | 0.0 | 0.61 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005629 | | | 0.27 Nlocal: 476.000 ave 476 max 476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8930.00 ave 8930 max 8930 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: 299508.0 ave 299508 max 299508 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 299508 Ave neighs/atom = 629.21849 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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 2 14 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.1544 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 83 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.899 | 5.899 | 5.899 Mbytes Step Temp E_pair E_mol TotEng Press Volume 83 0 -1669.2689 0 -1669.2689 -4086.6577 5633.0949 87 0 -1669.2999 0 -1669.2999 42.047022 5616.0964 Loop time of 0.0928209 on 1 procs for 4 steps with 476 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 = -1669.26890134517 -1669.29986157549 -1669.29986917257 Force two-norm initial, final = 26.484248 0.33690498 Force max component initial, final = 21.136795 0.20810131 Final line search alpha, max atom move = 0.0091505070 0.0019042324 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.090796 | 0.090796 | 0.090796 | 0.0 | 97.82 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00045373 | 0.00045373 | 0.00045373 | 0.0 | 0.49 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001571 | | | 1.69 Nlocal: 476.000 ave 476 max 476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9008.00 ave 9008 max 9008 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: 297976.0 ave 297976 max 297976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 297976 Ave neighs/atom = 626.00000 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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 2 13 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.1544 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) = 6.037 | 6.037 | 6.037 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1669.2999 0 -1669.2999 42.047022 Loop time of 1.884e-06 on 1 procs for 0 steps with 476 atoms 159.2% 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 | | 1.884e-06 | | |100.00 Nlocal: 476.000 ave 476 max 476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9064.00 ave 9064 max 9064 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: 298304.0 ave 298304 max 298304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 298304 Ave neighs/atom = 626.68908 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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 2 13 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.1544 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) = 6.037 | 6.037 | 6.037 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 -1669.2999 -1669.2999 8.0694429 78.830876 8.8286571 42.047022 42.047022 15.150078 51.673734 59.317252 2.3118836 260.56139 Loop time of 2.081e-06 on 1 procs for 0 steps with 476 atoms 192.2% 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 | | 2.081e-06 | | |100.00 Nlocal: 476.000 ave 476 max 476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9064.00 ave 9064 max 9064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 149152.0 ave 149152 max 149152 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 298304.0 ave 298304 max 298304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 298304 Ave neighs/atom = 626.68908 Neighbor list builds = 0 Dangerous builds = 0 476 -1669.29986917256 eV 2.31188355749411 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02