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 = 3.6111526 3.6111526 3.6111526 Created orthogonal box = (0.0000000 -39.060588 0.0000000) to (13.020196 39.060588 3.6111526) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0077677 5.0077677 3.6111526 Created 156 atoms using lattice units in orthogonal box = (0.0000000 -39.060588 0.0000000) to (13.020196 39.060588 3.6111526) create_atoms CPU = 0.002 seconds 156 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0077677 5.0077677 3.6111526 Created 158 atoms using lattice units in orthogonal box = (0.0000000 -39.060588 0.0000000) to (13.020196 39.060588 3.6111526) create_atoms CPU = 0.001 seconds 158 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 = 5 30 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 = 314 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_137964310702_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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 5 30 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) = 4.797 | 4.797 | 4.797 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1245.8048 0 -1245.8048 69826.26 78 0 -1327.5537 0 -1327.5537 16449.893 Loop time of 6.00887 on 1 procs for 78 steps with 314 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 = -1245.80482519976 -1327.55252859354 -1327.55373299102 Force two-norm initial, final = 114.14719 0.13947065 Force max component initial, final = 33.289931 0.033334889 Final line search alpha, max atom move = 1.0000000 0.033334889 Iterations, force evaluations = 78 146 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.995 | 5.995 | 5.995 | 0.0 | 99.77 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0075853 | 0.0075853 | 0.0075853 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006247 | | | 0.10 Nlocal: 314.000 ave 314 max 314 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2258.00 ave 2258 max 2258 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: 17068.0 ave 17068 max 17068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 17068 Ave neighs/atom = 54.356688 Neighbor list builds = 0 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 = 5 30 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 : 78 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.797 | 4.797 | 4.797 Mbytes Step Temp E_pair E_mol TotEng Press Volume 78 0 -1327.5537 0 -1327.5537 16449.893 3673.0948 90 0 -1327.95 0 -1327.95 -200.37872 3709.3927 Loop time of 0.573096 on 1 procs for 12 steps with 314 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1327.55373299102 -1327.94977174288 -1327.94995481581 Force two-norm initial, final = 76.450235 0.90245553 Force max component initial, final = 58.779041 0.51570318 Final line search alpha, max atom move = 0.0016248496 0.00083794011 Iterations, force evaluations = 12 13 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.57013 | 0.57013 | 0.57013 | 0.0 | 99.48 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0006473 | 0.0006473 | 0.0006473 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002321 | | | 0.41 Nlocal: 314.000 ave 314 max 314 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2274.00 ave 2274 max 2274 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: 17028.0 ave 17028 max 17028 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 17028 Ave neighs/atom = 54.229299 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 = 5 30 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) = 4.935 | 4.935 | 4.935 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1327.95 0 -1327.95 -200.37872 Loop time of 6.365e-06 on 1 procs for 0 steps with 314 atoms 172.8% 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 | | 6.365e-06 | | |100.00 Nlocal: 314.000 ave 314 max 314 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2278.00 ave 2278 max 2278 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: 16956.0 ave 16956 max 16956 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 16956 Ave neighs/atom = 54.000000 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 = 5 30 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) = 4.935 | 4.935 | 4.935 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 -1327.95 -1327.95 12.941005 78.573536 3.648031 -200.37872 -200.37872 -157.9219 -224.03449 -219.17979 2.2895615 146.69393 Loop time of 6.775e-06 on 1 procs for 0 steps with 314 atoms 250.9% 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 | | 6.775e-06 | | |100.00 Nlocal: 314.000 ave 314 max 314 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2278.00 ave 2278 max 2278 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 8478.00 ave 8478 max 8478 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 16956.0 ave 16956 max 16956 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 16956 Ave neighs/atom = 54.000000 Neighbor list builds = 0 Dangerous builds = 0 314 -1327.94995481581 eV 2.2895615487232 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:07