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 = 3.5483741 3.5483741 3.5483741 Created orthogonal box = (0.0000000 -41.075400 0.0000000) to (29.044694 41.075400 5.0181587) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6355376 6.1306567 5.0181587 Created 536 atoms using lattice units in orthogonal box = (0.0000000 -41.075400 0.0000000) to (29.044694 41.075400 5.0181587) create_atoms CPU = 0.006 seconds 536 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6355376 6.1306567 5.0181587 Created 538 atoms using lattice units in orthogonal box = (0.0000000 -41.075400 0.0000000) to (29.044694 41.075400 5.0181587) create_atoms CPU = 0.005 seconds 538 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 8 21 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 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1074 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_922363340570_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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 8 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 5.421 | 5.421 | 5.421 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4120.1198 0 -4120.1198 65651.733 82 0 -4335.3238 0 -4335.3238 19162.508 Loop time of 3.95277 on 1 procs for 82 steps with 1074 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 = -4120.11979532618 -4335.31972787337 -4335.32384802019 Force two-norm initial, final = 336.02363 0.18829631 Force max component initial, final = 92.240910 0.043464744 Final line search alpha, max atom move = 1.0000000 0.043464744 Iterations, force evaluations = 82 158 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.8696 | 3.8696 | 3.8696 | 0.0 | 97.90 Neigh | 0.030279 | 0.030279 | 0.030279 | 0.0 | 0.77 Comm | 0.029517 | 0.029517 | 0.029517 | 0.0 | 0.75 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02333 | | | 0.59 Nlocal: 1074.00 ave 1074 max 1074 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7400.00 ave 7400 max 7400 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: 211800.0 ave 211800 max 211800 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 211800 Ave neighs/atom = 197.20670 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 8 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 82 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.423 | 5.423 | 5.423 Mbytes Step Temp E_pair E_mol TotEng Press Volume 82 0 -4335.3238 0 -4335.3238 19162.508 11973.552 92 0 -4336.4849 0 -4336.4849 -79.98555 12063.838 Loop time of 0.343263 on 1 procs for 10 steps with 1074 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4335.32384802014 -4336.48486939012 -4336.48489664373 Force two-norm initial, final = 295.97215 1.3109572 Force max component initial, final = 271.27542 0.64975586 Final line search alpha, max atom move = 0.0016324748 0.0010607101 Iterations, force evaluations = 10 12 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.33219 | 0.33219 | 0.33219 | 0.0 | 96.77 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0023868 | 0.0023868 | 0.0023868 | 0.0 | 0.70 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008689 | | | 2.53 Nlocal: 1074.00 ave 1074 max 1074 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7400.00 ave 7400 max 7400 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: 211628.0 ave 211628 max 211628 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 211628 Ave neighs/atom = 197.04655 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 8 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 5.560 | 5.560 | 5.560 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4336.4849 0 -4336.4849 -79.98555 Loop time of 6.254e-06 on 1 procs for 0 steps with 1074 atoms 175.9% 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 | | 6.254e-06 | | |100.00 Nlocal: 1074.00 ave 1074 max 1074 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7400.00 ave 7400 max 7400 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: 210820.0 ave 210820 max 210820 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 210820 Ave neighs/atom = 196.29423 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 8 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 5.560 | 5.560 | 5.560 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 -4336.4849 -4336.4849 29.072555 82.874579 5.007039 -79.98555 -79.98555 -67.507404 -87.053173 -85.396074 2.3201136 532.76669 Loop time of 6.645e-06 on 1 procs for 0 steps with 1074 atoms 255.8% 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 | | 6.645e-06 | | |100.00 Nlocal: 1074.00 ave 1074 max 1074 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7400.00 ave 7400 max 7400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 105410.0 ave 105410 max 105410 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 210820.0 ave 210820 max 210820 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 210820 Ave neighs/atom = 196.29423 Neighbor list builds = 0 Dangerous builds = 0 1074 -4336.48489664373 eV 2.32011363919142 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05