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 = 4.0320825 4.0320825 4.0320825 Created orthogonal box = (0.0000000 -42.288838 0.0000000) to (51.793037 42.288838 9.8765446) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.5918411 6.1511037 6.5843631 Created 1320 atoms using lattice units in orthogonal box = (0.0000000 -42.288838 0.0000000) to (51.793037 42.288838 9.8765446) create_atoms CPU = 0.002 seconds 1320 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.5918411 6.1511037 6.5843631 Created 1326 atoms using lattice units in orthogonal box = (0.0000000 -42.288838 0.0000000) to (51.793037 42.288838 9.8765446) create_atoms CPU = 0.002 seconds 1326 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 = 7.5580544 ghost atom cutoff = 7.5580544 binsize = 3.7790272, bins = 14 23 3 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 7.558054418218096 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 18 atoms, new total = 2628 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_781138671863_002#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 = 7.5580544 ghost atom cutoff = 7.5580544 binsize = 3.7790272, bins = 14 23 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.558054418218096 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) = 5.961 | 5.961 | 5.961 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8565.2762 0 -8565.2762 6212.2849 60 0 -8801.8515 0 -8801.8515 773.08924 Loop time of 1.60088 on 1 procs for 60 steps with 2628 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8565.27622281365 -8801.84330276749 -8801.85154227808 Force two-norm initial, final = 67.874052 0.21588104 Force max component initial, final = 6.1625795 0.017493369 Final line search alpha, max atom move = 1.0000000 0.017493369 Iterations, force evaluations = 60 104 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.5305 | 1.5305 | 1.5305 | 0.0 | 95.60 Neigh | 0.047436 | 0.047436 | 0.047436 | 0.0 | 2.96 Comm | 0.0087331 | 0.0087331 | 0.0087331 | 0.0 | 0.55 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01426 | | | 0.89 Nlocal: 2628.00 ave 2628 max 2628 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7443.00 ave 7443 max 7443 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: 307632.0 ave 307632 max 307632 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 307632 Ave neighs/atom = 117.05936 Neighbor list builds = 2 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 = 7.5580544 ghost atom cutoff = 7.5580544 binsize = 3.7790272, bins = 14 23 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.558054418218096 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 60 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.964 | 5.964 | 5.964 Mbytes Step Temp E_pair E_mol TotEng Press Volume 60 0 -8801.8515 0 -8801.8515 773.08924 43264.546 63 0 -8801.9512 0 -8801.9512 -182.12609 43316.063 Loop time of 0.075871 on 1 procs for 3 steps with 2628 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 = -8801.85154227821 -8801.94411940452 -8801.95119598273 Force two-norm initial, final = 67.177113 8.7763341 Force max component initial, final = 60.692325 6.0635870 Final line search alpha, max atom move = 7.0871747e-05 0.00042973701 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.073523 | 0.073523 | 0.073523 | 0.0 | 96.91 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00032202 | 0.00032202 | 0.00032202 | 0.0 | 0.42 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002026 | | | 2.67 Nlocal: 2628.00 ave 2628 max 2628 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7671.00 ave 7671 max 7671 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: 326088.0 ave 326088 max 326088 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 326088 Ave neighs/atom = 124.08219 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 = 7.5580544 ghost atom cutoff = 7.5580544 binsize = 3.7790272, bins = 14 23 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.558054418218096 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) = 6.102 | 6.102 | 6.102 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8801.9512 0 -8801.9512 -182.12609 Loop time of 1.918e-06 on 1 procs for 0 steps with 2628 atoms 156.4% 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 | | 1.918e-06 | | |100.00 Nlocal: 2628.00 ave 2628 max 2628 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7671.00 ave 7671 max 7671 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: 322728.0 ave 322728 max 322728 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 322728 Ave neighs/atom = 122.80365 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 = 7.5580544 ghost atom cutoff = 7.5580544 binsize = 3.7790272, bins = 14 23 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.558054418218096 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) = 6.102 | 6.102 | 6.102 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 -8801.9512 -8801.9512 51.812022 84.79753 9.8590536 -182.12609 -182.12609 -200.46585 -122.02937 -223.88304 2.6202722 2465.4713 Loop time of 2.473e-06 on 1 procs for 0 steps with 2628 atoms 283.1% 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 | | 2.473e-06 | | |100.00 Nlocal: 2628.00 ave 2628 max 2628 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7671.00 ave 7671 max 7671 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 161364.0 ave 161364 max 161364 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 322728.0 ave 322728 max 322728 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 322728 Ave neighs/atom = 122.80365 Neighbor list builds = 0 Dangerous builds = 0 2628 -8801.95119598273 eV 2.62027222408221 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02