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 = 3.5242205 3.5242205 3.5242205 Created orthogonal box = (0.0000000 -45.132043 0.0000000) to (22.566021 45.132043 3.5242205) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9535169 4.9535169 3.5242205 Created 328 atoms using lattice units in orthogonal box = (0.0000000 -45.132043 0.0000000) to (22.566021 45.132043 3.5242205) create_atoms CPU = 0.002 seconds 328 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9535169 4.9535169 3.5242205 Created 330 atoms using lattice units in orthogonal box = (0.0000000 -45.132043 0.0000000) to (22.566021 45.132043 3.5242205) create_atoms CPU = 0.001 seconds 330 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 = 6.3171695 ghost atom cutoff = 6.3171695 binsize = 3.1585848, bins = 8 29 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 6.3171695 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 658 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_977363131043_005#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 = 6.3171695 ghost atom cutoff = 6.3171695 binsize = 3.1585848, bins = 8 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.3171695 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) = 4.515 | 4.515 | 4.515 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2868.6878 0 -2868.6878 14075.744 50 0 -2924.8708 0 -2924.8708 18926.237 Loop time of 0.658897 on 1 procs for 50 steps with 658 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 = -2868.68777806302 -2924.86796461152 -2924.87081103264 Force two-norm initial, final = 45.739635 0.18208725 Force max component initial, final = 7.8187325 0.030995768 Final line search alpha, max atom move = 1.0000000 0.030995768 Iterations, force evaluations = 50 90 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.63029 | 0.63029 | 0.63029 | 0.0 | 95.66 Neigh | 0.0094915 | 0.0094915 | 0.0094915 | 0.0 | 1.44 Comm | 0.010215 | 0.010215 | 0.010215 | 0.0 | 1.55 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008904 | | | 1.35 Nlocal: 658.000 ave 658 max 658 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4598.00 ave 4598 max 4598 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: 56732.0 ave 56732 max 56732 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 56732 Ave neighs/atom = 86.218845 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 = 6.3171695 ghost atom cutoff = 6.3171695 binsize = 3.1585848, bins = 8 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.3171695 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 50 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.515 | 4.515 | 4.515 Mbytes Step Temp E_pair E_mol TotEng Press Volume 50 0 -2924.8708 0 -2924.8708 18926.237 7178.4893 61 0 -2925.5134 0 -2925.5134 9.4395391 7245.5361 Loop time of 0.0959137 on 1 procs for 11 steps with 658 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 = -2924.87081103264 -2925.51300021532 -2925.51337099336 Force two-norm initial, final = 163.96831 0.60717921 Force max component initial, final = 144.21049 0.36098665 Final line search alpha, max atom move = 0.00021144247 7.6327907e-05 Iterations, force evaluations = 11 13 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.089635 | 0.089635 | 0.089635 | 0.0 | 93.45 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0014009 | 0.0014009 | 0.0014009 | 0.0 | 1.46 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004878 | | | 5.09 Nlocal: 658.000 ave 658 max 658 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4602.00 ave 4602 max 4602 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: 56560.0 ave 56560 max 56560 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 56560 Ave neighs/atom = 85.957447 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 = 6.3171695 ghost atom cutoff = 6.3171695 binsize = 3.1585848, bins = 8 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.3171695 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) = 4.653 | 4.653 | 4.653 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2925.5134 0 -2925.5134 9.4395391 Loop time of 6.505e-06 on 1 procs for 0 steps with 658 atoms 184.5% 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 | | 6.505e-06 | | |100.00 Nlocal: 658.000 ave 658 max 658 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4593.00 ave 4593 max 4593 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: 56512.0 ave 56512 max 56512 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 56512 Ave neighs/atom = 85.884498 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 = 6.3171695 ghost atom cutoff = 6.3171695 binsize = 3.1585848, bins = 8 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.3171695 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) = 4.653 | 4.653 | 4.653 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 -2925.5134 -2925.5134 22.610982 91.093418 3.517743 9.4395391 9.4395391 -63.90192 80.556944 11.663593 2.2576387 118.95889 Loop time of 6.886e-06 on 1 procs for 0 steps with 658 atoms 246.9% 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 | | 6.886e-06 | | |100.00 Nlocal: 658.000 ave 658 max 658 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4593.00 ave 4593 max 4593 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 28256.0 ave 28256 max 28256 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 56512.0 ave 56512 max 56512 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 56512 Ave neighs/atom = 85.884498 Neighbor list builds = 0 Dangerous builds = 0 658 -2925.51337099336 eV 2.25763871416082 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01