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 = 3.6473074 3.6473074 3.6473074 Created orthogonal box = (0.0000000 -36.835999 0.0000000) to (26.046985 36.835999 5.1580716) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.5965267 5.7781959 5.1580716 Created 408 atoms using lattice units in orthogonal box = (0.0000000 -36.835999 0.0000000) to (26.046985 36.835999 5.1580716) create_atoms CPU = 0.001 seconds 408 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.5965267 5.7781959 5.1580716 Created 410 atoms using lattice units in orthogonal box = (0.0000000 -36.835999 0.0000000) to (26.046985 36.835999 5.1580716) create_atoms CPU = 0.001 seconds 410 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, 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, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 0 atoms, new total = 818 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_608695023236_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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 10 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 4.909 | 4.909 | 4.909 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2891.4908 0 -2891.4908 130794.61 61 0 -3374.4867 0 -3374.4867 11968.17 Loop time of 4.47815 on 1 procs for 61 steps with 818 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 = -2891.49077220071 -3374.48372726323 -3374.48671901278 Force two-norm initial, final = 880.53387 0.23035315 Force max component initial, final = 198.61563 0.030567008 Final line search alpha, max atom move = 1.0000000 0.030567008 Iterations, force evaluations = 61 109 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.458 | 4.458 | 4.458 | 0.0 | 99.55 Neigh | 0.012757 | 0.012757 | 0.012757 | 0.0 | 0.28 Comm | 0.0032254 | 0.0032254 | 0.0032254 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004153 | | | 0.09 Nlocal: 818.000 ave 818 max 818 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3143.00 ave 3143 max 3143 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: 43908.0 ave 43908 max 43908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 43908 Ave neighs/atom = 53.677262 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 10 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 61 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.909 | 4.909 | 4.909 Mbytes Step Temp E_pair E_mol TotEng Press Volume 61 0 -3374.4867 0 -3374.4867 11968.17 9897.9959 72 0 -3375.1403 0 -3375.1403 26.99611 9968.5913 Loop time of 0.526074 on 1 procs for 11 steps with 818 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 = -3374.48671901278 -3375.14019291976 -3375.14031523774 Force two-norm initial, final = 158.44267 0.88485367 Force max component initial, final = 149.69784 0.22035030 Final line search alpha, max atom move = 0.00046924029 0.00010339724 Iterations, force evaluations = 11 12 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.52401 | 0.52401 | 0.52401 | 0.0 | 99.61 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00030799 | 0.00030799 | 0.00030799 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001758 | | | 0.33 Nlocal: 818.000 ave 818 max 818 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3156.00 ave 3156 max 3156 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: 43892.0 ave 43892 max 43892 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 43892 Ave neighs/atom = 53.657702 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 10 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 5.047 | 5.047 | 5.047 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3375.1403 0 -3375.1403 26.99611 Loop time of 2.114e-06 on 1 procs for 0 steps with 818 atoms 189.2% 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 | | 2.114e-06 | | |100.00 Nlocal: 818.000 ave 818 max 818 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3150.00 ave 3150 max 3150 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: 43828.0 ave 43828 max 43828 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 43828 Ave neighs/atom = 53.579462 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 10 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 5.047 | 5.047 | 5.047 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 -3375.1403 -3375.1403 25.975724 74.374271 5.1599252 26.99611 26.99611 35.318351 24.084617 21.585363 2.3361183 366.61679 Loop time of 1.691e-06 on 1 procs for 0 steps with 818 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 | | 1.691e-06 | | |100.00 Nlocal: 818.000 ave 818 max 818 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3150.00 ave 3150 max 3150 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 21914.0 ave 21914 max 21914 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 43828.0 ave 43828 max 43828 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 43828 Ave neighs/atom = 53.579462 Neighbor list builds = 0 Dangerous builds = 0 818 -3375.14031523774 eV 2.336118349701 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05