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 = 2.8603420 2.8603420 2.8603420 Created orthogonal box = (0.0000000 -37.074270 0.0000000) to (21.404840 37.074270 4.9542577) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.5867513 4.4136035 4.9542577 Created 336 atoms using lattice units in orthogonal box = (0.0000000 -37.074270 0.0000000) to (21.404840 37.074270 4.9542577) create_atoms CPU = 0.001 seconds 336 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.5867513 4.4136035 4.9542577 Created 339 atoms using lattice units in orthogonal box = (0.0000000 -37.074270 0.0000000) to (21.404840 37.074270 4.9542577) create_atoms CPU = 0.001 seconds 339 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 6 20 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 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 675 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_657255834688_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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 6 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 4.928 | 4.928 | 4.928 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2445.1724 0 -2445.1724 112940.47 241 0 -2953.9047 0 -2953.9047 -3079.4432 Loop time of 2.53079 on 1 procs for 241 steps with 675 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 = -2445.17236919658 -2953.9017501876 -2953.90469979724 Force two-norm initial, final = 755.60195 0.23416787 Force max component initial, final = 196.82087 0.076972575 Final line search alpha, max atom move = 1.0000000 0.076972575 Iterations, force evaluations = 241 420 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.4337 | 2.4337 | 2.4337 | 0.0 | 96.17 Neigh | 0.058426 | 0.058426 | 0.058426 | 0.0 | 2.31 Comm | 0.021794 | 0.021794 | 0.021794 | 0.0 | 0.86 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01683 | | | 0.67 Nlocal: 675.000 ave 675 max 675 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5175.00 ave 5175 max 5175 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: 111316.0 ave 111316 max 111316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 111316 Ave neighs/atom = 164.91259 Neighbor list builds = 8 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 6 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 241 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.928 | 4.928 | 4.928 Mbytes Step Temp E_pair E_mol TotEng Press Volume 241 0 -2953.9047 0 -2953.9047 -3079.4432 7863.0885 257 0 -2955.9087 0 -2955.9087 -12.196933 7847.2146 Loop time of 0.121284 on 1 procs for 16 steps with 675 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2953.90469979724 -2955.90740382468 -2955.90871060015 Force two-norm initial, final = 207.15512 2.4940941 Force max component initial, final = 147.66144 0.95753228 Final line search alpha, max atom move = 0.00041687038 0.00039916684 Iterations, force evaluations = 16 17 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.10904 | 0.10904 | 0.10904 | 0.0 | 89.90 Neigh | 0.0073611 | 0.0073611 | 0.0073611 | 0.0 | 6.07 Comm | 0.00090377 | 0.00090377 | 0.00090377 | 0.0 | 0.75 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003982 | | | 3.28 Nlocal: 675.000 ave 675 max 675 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5094.00 ave 5094 max 5094 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: 109588.0 ave 109588 max 109588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 109588 Ave neighs/atom = 162.35259 Neighbor list builds = 1 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 6 19 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 5.065 | 5.065 | 5.065 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2955.9087 0 -2955.9087 -12.196933 Loop time of 1.795e-06 on 1 procs for 0 steps with 675 atoms 167.1% 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 | | 1.795e-06 | | |100.00 Nlocal: 675.000 ave 675 max 675 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5094.00 ave 5094 max 5094 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: 109556.0 ave 109556 max 109556 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 109556 Ave neighs/atom = 162.30519 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 6 19 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 5.065 | 5.065 | 5.065 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 -2955.9087 -2955.9087 21.334847 73.11659 5.0304874 -12.196933 -12.196933 -37.930481 192.77982 -191.44014 2.2964594 3364.752 Loop time of 2.75e-06 on 1 procs for 0 steps with 675 atoms 254.5% 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 | | 2.75e-06 | | |100.00 Nlocal: 675.000 ave 675 max 675 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5094.00 ave 5094 max 5094 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 54778.0 ave 54778 max 54778 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 109556.0 ave 109556 max 109556 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 109556 Ave neighs/atom = 162.30519 Neighbor list builds = 0 Dangerous builds = 0 675 -2955.90871060015 eV 2.29645944462284 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02