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 -53.048723 0.0000000) to (18.755556 53.048723 4.0449272) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.7979329 4.9347649 4.0449272 Created 344 atoms using lattice units in orthogonal box = (0.0000000 -53.048723 0.0000000) to (18.755556 53.048723 4.0449272) create_atoms CPU = 0.002 seconds 344 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.7979329 4.9347649 4.0449272 Created 346 atoms using lattice units in orthogonal box = (0.0000000 -53.048723 0.0000000) to (18.755556 53.048723 4.0449272) create_atoms CPU = 0.001 seconds 346 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 = 8 40 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 2 atoms, new total = 688 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 = 8 40 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) = 4.895 | 4.895 | 4.895 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2526.2902 0 -2526.2902 75320.082 104 0 -2932.9034 0 -2932.9034 4607.4731 Loop time of 9.06113 on 1 procs for 104 steps with 688 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 = -2526.29021957791 -2932.90057900698 -2932.9033803048 Force two-norm initial, final = 759.61208 0.21945052 Force max component initial, final = 204.56896 0.043063297 Final line search alpha, max atom move = 1.0000000 0.043063297 Iterations, force evaluations = 104 193 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 9.0272 | 9.0272 | 9.0272 | 0.0 | 99.63 Neigh | 0.017418 | 0.017418 | 0.017418 | 0.0 | 0.19 Comm | 0.0082501 | 0.0082501 | 0.0082501 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008291 | | | 0.09 Nlocal: 688.000 ave 688 max 688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3534.00 ave 3534 max 3534 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: 39716.0 ave 39716 max 39716 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 39716 Ave neighs/atom = 57.726744 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 = 8 40 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 : 104 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.281 | 5.281 | 5.281 Mbytes Step Temp E_pair E_mol TotEng Press Volume 104 0 -2932.9034 0 -2932.9034 4607.4731 8049.0676 109 0 -2933.0113 0 -2933.0113 -39.989308 8069.779 Loop time of 0.343746 on 1 procs for 5 steps with 688 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 = -2932.9033803048 -2933.01120514467 -2933.01125008945 Force two-norm initial, final = 60.476165 0.58988109 Force max component initial, final = 59.936500 0.37550355 Final line search alpha, max atom move = 0.00089964053 0.00033781822 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.34223 | 0.34223 | 0.34223 | 0.0 | 99.56 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00027359 | 0.00027359 | 0.00027359 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001242 | | | 0.36 Nlocal: 688.000 ave 688 max 688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4060.00 ave 4060 max 4060 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: 39704.0 ave 39704 max 39704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 39704 Ave neighs/atom = 57.709302 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 = 8 40 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) = 5.419 | 5.419 | 5.419 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2933.0113 0 -2933.0113 -39.989308 Loop time of 1.616e-06 on 1 procs for 0 steps with 688 atoms 185.6% 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 | | 1.616e-06 | | |100.00 Nlocal: 688.000 ave 688 max 688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4060.00 ave 4060 max 4060 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: 39684.0 ave 39684 max 39684 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 39684 Ave neighs/atom = 57.680233 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 = 8 40 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) = 5.419 | 5.419 | 5.419 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 -2933.0113 -2933.0113 18.752168 106.48826 4.0411823 -39.989308 -39.989308 13.991162 -59.475514 -74.483573 2.2875552 389.51113 Loop time of 1.501e-06 on 1 procs for 0 steps with 688 atoms 133.2% 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 | | 1.501e-06 | | |100.00 Nlocal: 688.000 ave 688 max 688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4060.00 ave 4060 max 4060 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 19842.0 ave 19842 max 19842 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 39684.0 ave 39684 max 39684 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 39684 Ave neighs/atom = 57.680233 Neighbor list builds = 0 Dangerous builds = 0 688 -2933.01125008945 eV 2.28755524886645 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:09