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 = 2.8601955 2.8601955 2.8601955 Created orthogonal box = (0.0000000 -39.321186 0.0000000) to (10.701871 39.321186 7.0060194) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.5865163 4.3690207 4.6706796 Created 252 atoms using lattice units in orthogonal box = (0.0000000 -39.321186 0.0000000) to (10.701871 39.321186 7.0060194) create_atoms CPU = 0.001 seconds 252 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.5865163 4.3690207 4.6706796 Created 254 atoms using lattice units in orthogonal box = (0.0000000 -39.321186 0.0000000) to (10.701871 39.321186 7.0060194) create_atoms CPU = 0.001 seconds 254 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 3 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 = 506 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 3 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) = 4.833 | 4.833 | 4.833 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2007.7564 0 -2007.7564 56687.116 39 0 -2152.4171 0 -2152.4171 13599.008 Loop time of 2.56054 on 1 procs for 39 steps with 506 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2007.75641781133 -2152.415083971 -2152.41707612353 Force two-norm initial, final = 337.09564 0.18638908 Force max component initial, final = 161.36962 0.033869308 Final line search alpha, max atom move = 1.0000000 0.033869308 Iterations, force evaluations = 39 71 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.5558 | 2.5558 | 2.5558 | 0.0 | 99.82 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0020549 | 0.0020549 | 0.0020549 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002639 | | | 0.10 Nlocal: 506.000 ave 506 max 506 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2374.00 ave 2374 max 2374 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: 29316.0 ave 29316 max 29316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29316 Ave neighs/atom = 57.936759 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 3 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 : 39 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.833 | 4.833 | 4.833 Mbytes Step Temp E_pair E_mol TotEng Press Volume 39 0 -2152.4171 0 -2152.4171 13599.008 5896.41 52 0 -2153.0523 0 -2153.0523 588.87684 5939.0725 Loop time of 0.588172 on 1 procs for 13 steps with 506 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 = -2152.41707612353 -2153.0510793003 -2153.05228376666 Force two-norm initial, final = 118.00604 5.1238328 Force max component initial, final = 115.23982 4.6697549 Final line search alpha, max atom move = 0.0094584653 0.044168715 Iterations, force evaluations = 13 15 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.58572 | 0.58572 | 0.58572 | 0.0 | 99.58 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00036325 | 0.00036325 | 0.00036325 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002091 | | | 0.36 Nlocal: 506.000 ave 506 max 506 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2374.00 ave 2374 max 2374 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: 29136.0 ave 29136 max 29136 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29136 Ave neighs/atom = 57.581028 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 = 4 30 3 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) = 4.969 | 4.969 | 4.969 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2153.0523 0 -2153.0523 588.87684 Loop time of 2.062e-06 on 1 procs for 0 steps with 506 atoms 194.0% 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 | | 2.062e-06 | | |100.00 Nlocal: 506.000 ave 506 max 506 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2354.00 ave 2354 max 2354 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: 29132.0 ave 29132 max 29132 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29132 Ave neighs/atom = 57.573123 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 = 4 30 3 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) = 4.969 | 4.969 | 4.969 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 -2153.0523 -2153.0523 10.681234 79.557225 6.989041 588.87684 588.87684 1257.3249 542.02503 -32.719368 2.223405 369.39615 Loop time of 2.496e-06 on 1 procs for 0 steps with 506 atoms 160.3% 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 | | 2.496e-06 | | |100.00 Nlocal: 506.000 ave 506 max 506 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2354.00 ave 2354 max 2354 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 14566.0 ave 14566 max 14566 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 29132.0 ave 29132 max 29132 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29132 Ave neighs/atom = 57.573123 Neighbor list builds = 0 Dangerous builds = 0 506 -2153.05228376666 eV 2.22340495789298 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03