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 -39.401983 0.0000000) to (7.8803965 39.401983 3.5242205) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.7282379 4.7282379 3.5242205 Created 100 atoms using lattice units in orthogonal box = (0.0000000 -39.401983 0.0000000) to (7.8803965 39.401983 3.5242205) create_atoms CPU = 0.002 seconds 100 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.7282379 4.7282379 3.5242205 Created 102 atoms using lattice units in orthogonal box = (0.0000000 -39.401983 0.0000000) to (7.8803965 39.401983 3.5242205) create_atoms CPU = 0.001 seconds 102 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 = 3 25 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 2 atoms, new total = 200 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 = 3 25 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) = 4.414 | 4.414 | 4.414 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -881.13523 0 -881.13523 3552.4178 14 0 -887.67325 0 -887.67325 12884.181 Loop time of 0.0702467 on 1 procs for 14 steps with 200 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -881.135229161522 -887.67285080276 -887.673250301798 Force two-norm initial, final = 17.531333 0.060869174 Force max component initial, final = 6.1687124 0.0078899535 Final line search alpha, max atom move = 1.0000000 0.0078899535 Iterations, force evaluations = 14 26 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.067129 | 0.067129 | 0.067129 | 0.0 | 95.56 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0016805 | 0.0016805 | 0.0016805 | 0.0 | 2.39 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001437 | | | 2.05 Nlocal: 200.000 ave 200 max 200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2639.00 ave 2639 max 2639 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: 17296.0 ave 17296 max 17296 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 17296 Ave neighs/atom = 86.480000 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 = 6.3171695 ghost atom cutoff = 6.3171695 binsize = 3.1585848, bins = 3 25 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 : 14 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.413 | 4.413 | 4.413 Mbytes Step Temp E_pair E_mol TotEng Press Volume 14 0 -887.67325 0 -887.67325 12884.181 2188.5638 24 0 -887.83425 0 -887.83425 -142.39072 2202.8875 Loop time of 0.0322993 on 1 procs for 10 steps with 200 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 = -887.673250301795 -887.833386408764 -887.834248678299 Force two-norm initial, final = 39.312051 0.51316326 Force max component initial, final = 37.497537 0.38264247 Final line search alpha, max atom move = 0.00080679025 0.00030871222 Iterations, force evaluations = 10 11 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.029345 | 0.029345 | 0.029345 | 0.0 | 90.85 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00069902 | 0.00069902 | 0.00069902 | 0.0 | 2.16 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002255 | | | 6.98 Nlocal: 200.000 ave 200 max 200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2571.00 ave 2571 max 2571 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: 17224.0 ave 17224 max 17224 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 17224 Ave neighs/atom = 86.120000 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 = 3 26 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) = 4.552 | 4.552 | 4.552 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -887.83425 0 -887.83425 -142.39072 Loop time of 6.104e-06 on 1 procs for 0 steps with 200 atoms 196.6% 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 | | 6.104e-06 | | |100.00 Nlocal: 200.000 ave 200 max 200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2595.00 ave 2595 max 2595 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: 17192.0 ave 17192 max 17192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 17192 Ave neighs/atom = 85.960000 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 = 3 26 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) = 4.552 | 4.552 | 4.552 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 -887.83425 -887.83425 7.8696626 79.564479 3.5181714 -142.39072 -142.39072 64.47565 -280.9845 -210.66331 2.1791474 118.69273 Loop time of 6.906e-06 on 1 procs for 0 steps with 200 atoms 144.8% 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 | | 6.906e-06 | | |100.00 Nlocal: 200.000 ave 200 max 200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2595.00 ave 2595 max 2595 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 8596.00 ave 8596 max 8596 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 17192.0 ave 17192 max 17192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 17192 Ave neighs/atom = 85.960000 Neighbor list builds = 0 Dangerous builds = 0 200 -887.8342486783 eV 2.17914737232246 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00